Starting phenix.real_space_refine on Fri Jul 3 23:04:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gen_51295/07_2026/9gen_51295.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gen_51295/07_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_51295/07_2026/9gen_51295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gen_51295/07_2026/9gen_51295.map" model { file = "/net/cci-nas-00/data/ceres_data/9gen_51295/07_2026/9gen_51295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gen_51295/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.54, per 1000 atoms: 0.21 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: 1.48 Conformation dependent library (CDL) restraints added in 506.8 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: 2.23 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: 4.55 Time building geometry restraints manager: 1.99 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: 23846 1.60 - 3.19: 1023 3.19 - 4.79: 43 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: 0.750 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.600 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.150 ------------------------------------------------------------------------------- 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 : 0.669 7.986 24941 Z= 0.566 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 0.66657 / 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 : 0.463 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: 0.1559 time to fit residues: 40.6019 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 : 0.455 ------------------------------------------------------------------------------- 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: 10.0000 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** L 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.181238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.138958 restraints weight = 21604.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.142662 restraints weight = 11910.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145055 restraints weight = 8443.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.146272 restraints weight = 7020.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.147177 restraints weight = 6403.642| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17514 Z= 0.132 Angle : 0.552 8.141 24941 Z= 0.325 Chirality : 0.040 0.257 2803 Planarity : 0.004 0.033 2189 Dihedral : 28.493 171.547 4732 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.70 % Allowed : 24.07 % 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: 2.06 (0.24), residues: 1315 helix: 2.45 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.06 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 656 TYR 0.024 0.001 TYR D 80 PHE 0.010 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 0.54886 / 0.32 (24923) SS BOND : bond 0.00304 / 0.16 ( 6) SS BOND : angle 0.77517 / 0.34 ( 12) hydrogen bonds : bond 0.04804 / 3.23 ( 910) hydrogen bonds : angle 3.54906 / 2.53 ( 2324) link_NAG-ASN : bond 0.00596 / 0.40 ( 2) link_NAG-ASN : angle 3.97010 / 2.04 ( 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 197 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7802 (pt0) cc_final: 0.7300 (pm20) REVERT: B 25 ASN cc_start: 0.8442 (t0) cc_final: 0.8221 (t0) REVERT: B 92 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8427 (ttp80) REVERT: D 79 HIS cc_start: 0.8184 (t-90) cc_final: 0.7764 (t-170) REVERT: D 83 ARG cc_start: 0.7729 (mmt90) cc_final: 0.7334 (mtp-110) REVERT: E 77 ASP cc_start: 0.8415 (m-30) cc_final: 0.7951 (t0) REVERT: G 95 LYS cc_start: 0.8608 (tttt) cc_final: 0.8383 (tttm) REVERT: L 202 GLU cc_start: 0.7837 (tp30) cc_final: 0.7562 (tp30) REVERT: L 345 SER cc_start: 0.8807 (m) cc_final: 0.8428 (t) REVERT: L 409 MET cc_start: 0.7724 (mtp) cc_final: 0.7444 (mtm) REVERT: L 530 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8273 (p) REVERT: L 631 MET cc_start: 0.8803 (mmt) cc_final: 0.8527 (mmt) REVERT: L 696 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7923 (tp40) REVERT: L 726 ASP cc_start: 0.7998 (p0) cc_final: 0.7420 (p0) outliers start: 42 outliers final: 20 residues processed: 188 average time/residue: 0.1505 time to fit residues: 41.5643 Evaluate side-chains 168 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 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 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 325 THR Chi-restraints excluded: chain L residue 389 LEU 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: 8.9990 chunk 138 optimal weight: 3.9990 chunk 147 optimal weight: 0.0970 chunk 115 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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** L 299 ASN L 372 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.172520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.132705 restraints weight = 21513.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.135773 restraints weight = 12815.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137740 restraints weight = 9576.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.138715 restraints weight = 8191.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139415 restraints weight = 7580.780| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 17514 Z= 0.257 Angle : 0.684 8.262 24941 Z= 0.375 Chirality : 0.044 0.257 2803 Planarity : 0.005 0.041 2189 Dihedral : 28.837 171.391 4706 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.73 % Allowed : 24.34 % Favored : 69.93 % 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: 1.81 (0.24), residues: 1315 helix: 2.25 (0.19), residues: 739 sheet: None (None), residues: 0 loop : -0.18 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 473 TYR 0.041 0.003 TYR D 80 PHE 0.015 0.001 PHE L 252 TRP 0.006 0.001 TRP L 643 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.26 (17506) covalent geometry : angle 0.68102 / 0.37 (24923) SS BOND : bond 0.00321 / 0.20 ( 6) SS BOND : angle 0.64629 / 0.26 ( 12) hydrogen bonds : bond 0.05431 / 3.68 ( 910) hydrogen bonds : angle 3.69234 / 2.67 ( 2324) link_NAG-ASN : bond 0.00349 / 0.23 ( 2) link_NAG-ASN : angle 4.03353 / 2.05 ( 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 227 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 162 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7931 (pt0) cc_final: 0.7623 (pm20) REVERT: B 25 ASN cc_start: 0.8482 (t0) cc_final: 0.8279 (t0) REVERT: D 79 HIS cc_start: 0.8361 (t-90) cc_final: 0.7919 (t-170) REVERT: D 83 ARG cc_start: 0.7725 (mmt90) cc_final: 0.7490 (mtm-85) REVERT: E 71 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8254 (t) REVERT: F 92 ARG cc_start: 0.8756 (ttp80) cc_final: 0.8506 (ttp80) REVERT: G 38 ASN cc_start: 0.8376 (m110) cc_final: 0.8170 (m110) REVERT: G 104 GLN cc_start: 0.8836 (mt0) cc_final: 0.8609 (mt0) REVERT: L 202 GLU cc_start: 0.7733 (tp30) cc_final: 0.7527 (tp30) REVERT: L 345 SER cc_start: 0.8756 (m) cc_final: 0.8421 (t) REVERT: L 409 MET cc_start: 0.7902 (mtp) cc_final: 0.7583 (mtm) REVERT: L 484 ASP cc_start: 0.7426 (p0) cc_final: 0.7180 (p0) REVERT: L 530 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8468 (p) REVERT: L 631 MET cc_start: 0.8816 (mmt) cc_final: 0.8574 (mmt) REVERT: L 726 ASP cc_start: 0.7998 (p0) cc_final: 0.7446 (p0) outliers start: 65 outliers final: 46 residues processed: 215 average time/residue: 0.1380 time to fit residues: 43.9920 Evaluate side-chains 208 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 D residue 33 SER 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 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 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 404 THR Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 458 THR Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 486 VAL 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 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: 9.9990 chunk 112 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 102 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.182804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.139931 restraints weight = 21472.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.143356 restraints weight = 12402.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145591 restraints weight = 9106.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146866 restraints weight = 7705.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147459 restraints weight = 7062.859| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17514 Z= 0.134 Angle : 0.556 8.124 24941 Z= 0.321 Chirality : 0.040 0.247 2803 Planarity : 0.004 0.042 2189 Dihedral : 28.674 171.106 4703 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.53 % Allowed : 26.54 % Favored : 69.93 % 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: 2.49 (0.19), residues: 743 sheet: None (None), residues: 0 loop : -0.08 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.043 0.002 TYR D 80 PHE 0.012 0.001 PHE E 67 TRP 0.010 0.001 TRP L 602 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (17506) covalent geometry : angle 0.55289 / 0.32 (24923) SS BOND : bond 0.00251 / 0.14 ( 6) SS BOND : angle 0.56557 / 0.27 ( 12) hydrogen bonds : bond 0.04533 / 3.06 ( 910) hydrogen bonds : angle 3.37241 / 2.42 ( 2324) link_NAG-ASN : bond 0.00520 / 0.35 ( 2) link_NAG-ASN : angle 4.01795 / 2.06 ( 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 202 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7888 (pt0) cc_final: 0.7504 (pm20) REVERT: B 25 ASN cc_start: 0.8474 (t0) cc_final: 0.7951 (t0) REVERT: B 92 ARG cc_start: 0.8743 (ttp80) cc_final: 0.8402 (ttp80) REVERT: D 83 ARG cc_start: 0.7763 (mmt90) cc_final: 0.7388 (mtm-85) REVERT: E 71 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8234 (t) REVERT: E 73 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: F 92 ARG cc_start: 0.8625 (ttp80) cc_final: 0.8409 (ttp80) REVERT: G 38 ASN cc_start: 0.8304 (m110) cc_final: 0.8045 (m110) REVERT: G 104 GLN cc_start: 0.8769 (mt0) cc_final: 0.8524 (mt0) REVERT: L 184 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7856 (tpp80) REVERT: L 202 GLU cc_start: 0.7726 (tp30) cc_final: 0.7453 (tp30) REVERT: L 345 SER cc_start: 0.8763 (m) cc_final: 0.8383 (t) REVERT: L 409 MET cc_start: 0.7845 (mtp) cc_final: 0.7572 (mtm) REVERT: L 422 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8035 (tm-30) REVERT: L 530 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8430 (p) REVERT: L 631 MET cc_start: 0.8854 (mmp) cc_final: 0.8650 (mmt) REVERT: L 738 LEU cc_start: 0.8298 (mp) cc_final: 0.7953 (mt) outliers start: 40 outliers final: 25 residues processed: 196 average time/residue: 0.1384 time to fit residues: 40.1793 Evaluate side-chains 182 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL 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 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 175 THR Chi-restraints excluded: chain L residue 177 THR 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 325 THR Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain L residue 654 LYS Chi-restraints excluded: chain L residue 703 ILE 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: 10.0000 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.182919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.140145 restraints weight = 21299.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143541 restraints weight = 12316.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.145748 restraints weight = 9060.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.147023 restraints weight = 7687.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147560 restraints weight = 7051.957| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1282 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= 0.135 Angle : 0.554 8.061 24941 Z= 0.317 Chirality : 0.039 0.253 2803 Planarity : 0.004 0.041 2189 Dihedral : 28.678 170.912 4703 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.53 % Allowed : 27.07 % Favored : 69.40 % 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: 2.13 (0.24), residues: 1315 helix: 2.53 (0.19), residues: 745 sheet: None (None), residues: 0 loop : -0.09 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.046 0.002 TYR D 80 PHE 0.012 0.001 PHE E 67 TRP 0.008 0.001 TRP L 602 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (17506) covalent geometry : angle 0.55117 / 0.32 (24923) SS BOND : bond 0.00264 / 0.15 ( 6) SS BOND : angle 0.54769 / 0.27 ( 12) hydrogen bonds : bond 0.04379 / 2.97 ( 910) hydrogen bonds : angle 3.29488 / 2.36 ( 2324) link_NAG-ASN : bond 0.00558 / 0.38 ( 2) link_NAG-ASN : angle 3.93861 / 2.02 ( 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 189 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7867 (pt0) cc_final: 0.7515 (pm20) REVERT: B 25 ASN cc_start: 0.8433 (t0) cc_final: 0.7940 (t0) REVERT: D 56 MET cc_start: 0.8451 (tpp) cc_final: 0.7986 (tpp) REVERT: D 83 ARG cc_start: 0.7661 (mmt90) cc_final: 0.7300 (mtm-85) REVERT: E 71 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8214 (t) REVERT: E 73 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: G 38 ASN cc_start: 0.8236 (m110) cc_final: 0.7920 (m110) REVERT: G 104 GLN cc_start: 0.8736 (mt0) cc_final: 0.8508 (mt0) REVERT: L 202 GLU cc_start: 0.7662 (tp30) cc_final: 0.7431 (tp30) REVERT: L 345 SER cc_start: 0.8746 (m) cc_final: 0.8362 (t) REVERT: L 409 MET cc_start: 0.7841 (mtp) cc_final: 0.7542 (mtm) REVERT: L 422 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8052 (tm-30) REVERT: L 530 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8449 (p) REVERT: L 726 ASP cc_start: 0.7871 (p0) cc_final: 0.7348 (p0) REVERT: L 738 LEU cc_start: 0.8240 (mp) cc_final: 0.7890 (mt) outliers start: 40 outliers final: 30 residues processed: 184 average time/residue: 0.1331 time to fit residues: 36.9409 Evaluate side-chains 180 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 79 ILE 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 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 G residue 107 VAL Chi-restraints excluded: chain H residue 87 THR 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 281 CYS Chi-restraints excluded: chain L residue 286 VAL 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 430 LEU 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: 0.0050 chunk 148 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.177886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135916 restraints weight = 21614.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.139520 restraints weight = 11985.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141641 restraints weight = 8599.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143122 restraints weight = 7239.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143798 restraints weight = 6581.089| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17514 Z= 0.121 Angle : 0.536 7.765 24941 Z= 0.310 Chirality : 0.039 0.249 2803 Planarity : 0.004 0.038 2189 Dihedral : 28.638 170.787 4703 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.17 % Allowed : 27.51 % Favored : 69.31 % 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: 2.22 (0.24), residues: 1315 helix: 2.64 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -0.10 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 92 TYR 0.049 0.001 TYR D 80 PHE 0.011 0.001 PHE E 67 TRP 0.008 0.001 TRP L 602 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.12 (17506) covalent geometry : angle 0.53225 / 0.31 (24923) SS BOND : bond 0.00273 / 0.15 ( 6) SS BOND : angle 0.53352 / 0.29 ( 12) hydrogen bonds : bond 0.04211 / 2.84 ( 910) hydrogen bonds : angle 3.20032 / 2.28 ( 2324) link_NAG-ASN : bond 0.00573 / 0.38 ( 2) link_NAG-ASN : angle 3.83479 / 1.97 ( 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 187 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7831 (pt0) cc_final: 0.7353 (pm20) REVERT: B 25 ASN cc_start: 0.8510 (t0) cc_final: 0.7983 (t0) REVERT: D 83 ARG cc_start: 0.7732 (mmt90) cc_final: 0.7194 (mtm-85) REVERT: E 71 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8106 (t) REVERT: E 73 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: E 77 ASP cc_start: 0.8451 (m-30) cc_final: 0.8007 (t0) REVERT: F 77 LYS cc_start: 0.9041 (mttm) cc_final: 0.8779 (tppp) REVERT: F 92 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8018 (tmm160) REVERT: L 202 GLU cc_start: 0.7792 (tp30) cc_final: 0.7527 (tp30) REVERT: L 345 SER cc_start: 0.8714 (m) cc_final: 0.8317 (t) REVERT: L 409 MET cc_start: 0.7691 (mtp) cc_final: 0.7476 (mtm) REVERT: L 422 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8036 (tm-30) REVERT: L 631 MET cc_start: 0.8438 (mmt) cc_final: 0.7901 (mmt) REVERT: L 726 ASP cc_start: 0.8043 (p0) cc_final: 0.7403 (p0) outliers start: 36 outliers final: 26 residues processed: 180 average time/residue: 0.1298 time to fit residues: 34.9943 Evaluate side-chains 171 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 79 ILE 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 71 VAL Chi-restraints excluded: chain E residue 73 GLU 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 G residue 107 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 175 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 281 CYS Chi-restraints excluded: chain L residue 286 VAL 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 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 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: 2.9990 chunk 10 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN H 46 HIS L 299 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.172901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.129655 restraints weight = 21422.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132688 restraints weight = 12950.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134687 restraints weight = 9736.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.135838 restraints weight = 8349.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136383 restraints weight = 7695.144| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 17514 Z= 0.342 Angle : 0.800 10.159 24941 Z= 0.425 Chirality : 0.049 0.294 2803 Planarity : 0.006 0.039 2189 Dihedral : 29.063 170.712 4702 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.85 % Allowed : 26.46 % 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: 1.37 (0.23), residues: 1315 helix: 1.87 (0.19), residues: 743 sheet: None (None), residues: 0 loop : -0.35 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 92 TYR 0.056 0.003 TYR D 80 PHE 0.015 0.002 PHE L 252 TRP 0.007 0.002 TRP L 602 HIS 0.013 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00793 / 0.34 (17506) covalent geometry : angle 0.79749 / 0.42 (24923) SS BOND : bond 0.00439 / 0.26 ( 6) SS BOND : angle 0.68160 / 0.30 ( 12) hydrogen bonds : bond 0.06013 / 4.08 ( 910) hydrogen bonds : angle 3.85914 / 2.80 ( 2324) link_NAG-ASN : bond 0.00383 / 0.26 ( 2) link_NAG-ASN : angle 4.18479 / 2.09 ( 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 212 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 157 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7926 (pt0) cc_final: 0.7615 (pm20) REVERT: D 83 ARG cc_start: 0.7803 (mmt90) cc_final: 0.7496 (mtm-85) REVERT: E 71 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8355 (t) REVERT: G 38 ASN cc_start: 0.8507 (m-40) cc_final: 0.8196 (m110) REVERT: G 104 GLN cc_start: 0.8850 (mt0) cc_final: 0.8638 (mt0) REVERT: L 202 GLU cc_start: 0.7727 (tp30) cc_final: 0.7500 (tp30) REVERT: L 409 MET cc_start: 0.7832 (mtp) cc_final: 0.7564 (mtm) REVERT: L 422 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8181 (tm-30) REVERT: L 437 TRP cc_start: 0.7967 (OUTLIER) cc_final: 0.7336 (m-10) REVERT: L 440 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7153 (tm-30) REVERT: L 726 ASP cc_start: 0.8112 (p0) cc_final: 0.7577 (p0) outliers start: 55 outliers final: 42 residues processed: 200 average time/residue: 0.1193 time to fit residues: 36.1934 Evaluate side-chains 193 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 79 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 VAL 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 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 404 THR Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 493 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 13 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 108 ASN D 44 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131778 restraints weight = 21516.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135365 restraints weight = 12032.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.137655 restraints weight = 8659.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.138948 restraints weight = 7245.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139442 restraints weight = 6604.428| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17514 Z= 0.139 Angle : 0.584 8.257 24941 Z= 0.332 Chirality : 0.041 0.244 2803 Planarity : 0.004 0.041 2189 Dihedral : 28.800 170.964 4702 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.73 % Allowed : 28.31 % Favored : 68.96 % 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: 1.91 (0.24), residues: 1315 helix: 2.35 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -0.18 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 92 TYR 0.026 0.002 TYR D 37 PHE 0.013 0.001 PHE E 67 TRP 0.012 0.001 TRP L 602 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (17506) covalent geometry : angle 0.58056 / 0.33 (24923) SS BOND : bond 0.00311 / 0.17 ( 6) SS BOND : angle 0.57734 / 0.29 ( 12) hydrogen bonds : bond 0.04512 / 3.06 ( 910) hydrogen bonds : angle 3.38355 / 2.41 ( 2324) link_NAG-ASN : bond 0.00540 / 0.36 ( 2) link_NAG-ASN : angle 4.10742 / 2.11 ( 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 185 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7954 (pt0) cc_final: 0.7588 (pm20) REVERT: B 25 ASN cc_start: 0.8615 (t0) cc_final: 0.8184 (t0) REVERT: B 50 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8525 (tt) REVERT: D 83 ARG cc_start: 0.7805 (mmt90) cc_final: 0.7434 (mtm-85) REVERT: E 71 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8241 (t) REVERT: G 38 ASN cc_start: 0.8423 (m-40) cc_final: 0.8103 (m110) REVERT: G 104 GLN cc_start: 0.8802 (mt0) cc_final: 0.8598 (mt0) REVERT: L 202 GLU cc_start: 0.7755 (tp30) cc_final: 0.7517 (tp30) REVERT: L 345 SER cc_start: 0.8730 (m) cc_final: 0.8315 (t) REVERT: L 409 MET cc_start: 0.7741 (mtp) cc_final: 0.7489 (mtm) REVERT: L 422 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7961 (tm-30) REVERT: L 437 TRP cc_start: 0.7874 (OUTLIER) cc_final: 0.7331 (m-10) outliers start: 31 outliers final: 24 residues processed: 181 average time/residue: 0.1309 time to fit residues: 35.5374 Evaluate side-chains 175 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 50 ILE 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 87 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 VAL 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 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 303 ILE Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 619 THR Chi-restraints excluded: chain L residue 654 LYS Chi-restraints excluded: chain L residue 717 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 0.0670 chunk 110 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.176327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133891 restraints weight = 21566.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137536 restraints weight = 12005.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.139802 restraints weight = 8592.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.141259 restraints weight = 7188.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.141927 restraints weight = 6533.914| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17514 Z= 0.130 Angle : 0.566 9.767 24941 Z= 0.320 Chirality : 0.040 0.253 2803 Planarity : 0.004 0.035 2189 Dihedral : 28.756 170.517 4702 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.00 % Allowed : 28.04 % Favored : 68.96 % 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: 2.07 (0.24), residues: 1315 helix: 2.53 (0.19), residues: 743 sheet: None (None), residues: 0 loop : -0.17 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 248 TYR 0.022 0.001 TYR H 80 PHE 0.013 0.001 PHE E 67 TRP 0.010 0.001 TRP L 602 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (17506) covalent geometry : angle 0.56254 / 0.32 (24923) SS BOND : bond 0.00277 / 0.15 ( 6) SS BOND : angle 0.56453 / 0.28 ( 12) hydrogen bonds : bond 0.04256 / 2.92 ( 910) hydrogen bonds : angle 3.26927 / 2.32 ( 2324) link_NAG-ASN : bond 0.00581 / 0.39 ( 2) link_NAG-ASN : angle 3.80383 / 1.96 ( 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 186 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7830 (pt0) cc_final: 0.7419 (pm20) REVERT: B 25 ASN cc_start: 0.8616 (t0) cc_final: 0.8278 (t0) REVERT: B 50 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8474 (tt) REVERT: D 79 HIS cc_start: 0.8363 (t-90) cc_final: 0.8081 (t-170) REVERT: D 83 ARG cc_start: 0.7743 (mmt90) cc_final: 0.7333 (mtm-85) REVERT: E 71 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8183 (t) REVERT: F 77 LYS cc_start: 0.9057 (mttm) cc_final: 0.8813 (tppp) REVERT: H 118 TYR cc_start: 0.8461 (t80) cc_final: 0.8200 (t80) REVERT: L 202 GLU cc_start: 0.7773 (tp30) cc_final: 0.7526 (tp30) REVERT: L 345 SER cc_start: 0.8676 (m) cc_final: 0.8289 (t) REVERT: L 409 MET cc_start: 0.7645 (mtp) cc_final: 0.7437 (mtm) REVERT: L 422 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7928 (tm-30) REVERT: L 726 ASP cc_start: 0.8102 (p0) cc_final: 0.7817 (p0) outliers start: 34 outliers final: 25 residues processed: 180 average time/residue: 0.1298 time to fit residues: 34.4717 Evaluate side-chains 174 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 71 VAL 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 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 357 SER Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 588 MET Chi-restraints excluded: chain L residue 619 THR Chi-restraints excluded: chain L residue 654 LYS Chi-restraints excluded: chain L residue 717 ILE Chi-restraints excluded: chain L residue 722 SER 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: 0.6980 chunk 121 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 111 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.176945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.135058 restraints weight = 21558.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138650 restraints weight = 12056.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140973 restraints weight = 8614.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.142347 restraints weight = 7195.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143040 restraints weight = 6523.153| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17514 Z= 0.127 Angle : 0.568 9.928 24941 Z= 0.321 Chirality : 0.040 0.248 2803 Planarity : 0.004 0.036 2189 Dihedral : 28.741 170.567 4702 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.03 % Allowed : 29.37 % 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: 2.12 (0.24), residues: 1315 helix: 2.57 (0.19), residues: 743 sheet: None (None), residues: 0 loop : -0.15 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 92 TYR 0.033 0.001 TYR D 37 PHE 0.012 0.001 PHE E 67 TRP 0.010 0.001 TRP L 602 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (17506) covalent geometry : angle 0.56521 / 0.32 (24923) SS BOND : bond 0.00272 / 0.15 ( 6) SS BOND : angle 0.55855 / 0.28 ( 12) hydrogen bonds : bond 0.04193 / 2.85 ( 910) hydrogen bonds : angle 3.24044 / 2.29 ( 2324) link_NAG-ASN : bond 0.00572 / 0.38 ( 2) link_NAG-ASN : angle 3.84168 / 2.00 ( 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 169 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7920 (pt0) cc_final: 0.7440 (pm20) REVERT: B 25 ASN cc_start: 0.8683 (t0) cc_final: 0.8340 (t0) REVERT: D 83 ARG cc_start: 0.7680 (mmt90) cc_final: 0.7126 (mtm-85) REVERT: E 71 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8092 (t) REVERT: E 77 ASP cc_start: 0.8332 (t0) cc_final: 0.7814 (t0) REVERT: F 77 LYS cc_start: 0.9103 (mttm) cc_final: 0.8849 (tppp) REVERT: H 118 TYR cc_start: 0.8449 (t80) cc_final: 0.8190 (t80) REVERT: L 202 GLU cc_start: 0.7852 (tp30) cc_final: 0.7561 (tp30) REVERT: L 345 SER cc_start: 0.8644 (m) cc_final: 0.8244 (t) REVERT: L 409 MET cc_start: 0.7586 (mtp) cc_final: 0.7361 (mtm) REVERT: L 726 ASP cc_start: 0.8196 (p0) cc_final: 0.7924 (p0) outliers start: 23 outliers final: 21 residues processed: 168 average time/residue: 0.1261 time to fit residues: 31.7524 Evaluate side-chains 166 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 71 VAL 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 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 654 LYS Chi-restraints excluded: chain L residue 717 ILE Chi-restraints excluded: chain L residue 722 SER 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: 0.5980 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.176794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134473 restraints weight = 21575.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138080 restraints weight = 11999.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.140378 restraints weight = 8614.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.141624 restraints weight = 7215.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.142452 restraints weight = 6591.417| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17514 Z= 0.131 Angle : 0.562 9.442 24941 Z= 0.319 Chirality : 0.039 0.249 2803 Planarity : 0.004 0.034 2189 Dihedral : 28.752 170.520 4702 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.38 % Allowed : 28.84 % Favored : 68.78 % 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: 2.16 (0.24), residues: 1315 helix: 2.61 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -0.15 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 92 TYR 0.032 0.002 TYR D 37 PHE 0.012 0.001 PHE E 67 TRP 0.009 0.001 TRP L 602 HIS 0.008 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (17506) covalent geometry : angle 0.55891 / 0.32 (24923) SS BOND : bond 0.00266 / 0.15 ( 6) SS BOND : angle 0.55231 / 0.28 ( 12) hydrogen bonds : bond 0.04190 / 2.86 ( 910) hydrogen bonds : angle 3.24842 / 2.30 ( 2324) link_NAG-ASN : bond 0.00550 / 0.37 ( 2) link_NAG-ASN : angle 3.82223 / 1.98 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2219.73 seconds wall clock time: 39 minutes 11.93 seconds (2351.93 seconds total)