Starting phenix.real_space_refine on Sun Aug 24 03:51:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gen_51295/08_2025/9gen_51295.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gen_51295/08_2025/9gen_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 { model { file = "/net/cci-nas-00/data/ceres_data/9gen_51295/08_2025/9gen_51295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gen_51295/08_2025/9gen_51295.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gen_51295/08_2025/9gen_51295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gen_51295/08_2025/9gen_51295.map" } 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-2.0-5787/lib/python3.9/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: 3.99, per 1000 atoms: 0.24 Number of scatterers: 16590 At special positions: 0 Unit cell: (125.84, 116.16, 125.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 290 15.00 O 3639 8.00 N 3092 7.00 C 9525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 167 " - pdb=" SG CYS L 180 " distance=2.03 Simple disulfide: pdb=" SG CYS L 281 " - pdb=" SG CYS L 291 " distance=2.03 Simple disulfide: pdb=" SG CYS L 285 " - pdb=" SG CYS L 309 " distance=2.03 Simple disulfide: pdb=" SG CYS L 387 " - pdb=" SG CYS L 398 " distance=2.03 Simple disulfide: pdb=" SG CYS L 606 " - pdb=" SG CYS L 663 " distance=2.03 Simple disulfide: pdb=" SG CYS L 704 " - pdb=" SG CYS L 730 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG L 801 " - " ASN L 483 " " NAG L 802 " - " ASN L 391 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 557.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.69 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: 4.77 Time building geometry restraints manager: 1.91 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' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" C ASP L 544 " pdb=" N PRO L 545 " ideal model delta sigma weight residual 1.336 1.351 -0.016 1.23e-02 6.61e+03 1.66e+00 bond pdb=" CB ASN C 110 " pdb=" CG ASN C 110 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.42e+00 bond pdb=" CB ASN F 25 " pdb=" CG ASN F 25 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.36e+00 bond pdb=" CB ASN G 110 " pdb=" CG ASN G 110 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.30e+00 ... (remaining 17501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 24404 1.60 - 3.19: 472 3.19 - 4.79: 36 4.79 - 6.39: 6 6.39 - 7.99: 5 Bond angle restraints: 24923 Sorted by residual: angle pdb=" C HIS H 79 " pdb=" N TYR H 80 " pdb=" CA TYR H 80 " ideal model delta sigma weight residual 120.68 126.29 -5.61 1.70e+00 3.46e-01 1.09e+01 angle pdb=" N VAL L 342 " pdb=" CA VAL L 342 " pdb=" C VAL L 342 " ideal model delta sigma weight residual 113.20 110.39 2.81 9.60e-01 1.09e+00 8.60e+00 angle pdb=" CB MET D 59 " pdb=" CG MET D 59 " pdb=" SD MET D 59 " ideal model delta sigma weight residual 112.70 120.69 -7.99 3.00e+00 1.11e-01 7.09e+00 angle pdb=" C GLY L 278 " pdb=" N VAL L 279 " pdb=" CA VAL L 279 " ideal model delta sigma weight residual 121.97 126.69 -4.72 1.80e+00 3.09e-01 6.88e+00 angle pdb=" CA ASN F 25 " pdb=" CB ASN F 25 " pdb=" CG ASN F 25 " ideal model delta sigma weight residual 112.60 115.21 -2.61 1.00e+00 1.00e+00 6.84e+00 ... (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: 2296 0.042 - 0.083: 414 0.083 - 0.125: 86 0.125 - 0.166: 6 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=" CA ASP H 48 " pdb=" N ASP H 48 " pdb=" C ASP H 48 " pdb=" CB ASP H 48 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.29e-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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.870 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.003 0.040 17514 Z= 0.135 Angle : 0.534 7.986 24941 Z= 0.309 Chirality : 0.034 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 aren 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 covalent geometry : bond 0.00284 (17506) covalent geometry : angle 0.53028 (24923) SS BOND : bond 0.00249 ( 6) SS BOND : angle 0.50925 ( 12) hydrogen bonds : bond 0.11277 ( 910) hydrogen bonds : angle 4.68043 ( 2324) link_NAG-ASN : bond 0.00574 ( 2) link_NAG-ASN : angle 3.84597 ( 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 : 0.475 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: 0.1615 time to fit residues: 41.6681 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 : 0.486 ------------------------------------------------------------------------------- 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: 7.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.0170 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN E 113 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 329 GLN L 502 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.190992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.148525 restraints weight = 22939.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.152359 restraints weight = 12525.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.154840 restraints weight = 8852.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156131 restraints weight = 7330.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.157111 restraints weight = 6675.193| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17514 Z= 0.130 Angle : 0.508 7.900 24941 Z= 0.293 Chirality : 0.033 0.210 2803 Planarity : 0.004 0.034 2189 Dihedral : 28.205 169.970 4732 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.17 % Allowed : 23.99 % Favored : 72.84 % 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 aren not related in a simple way. whole: 2.21 (0.24), residues: 1315 helix: 2.59 (0.19), residues: 745 sheet: None (None), residues: 0 loop : -0.03 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.024 0.001 TYR D 80 PHE 0.009 0.001 PHE E 67 TRP 0.008 0.001 TRP L 602 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00281 (17506) covalent geometry : angle 0.50446 (24923) SS BOND : bond 0.00270 ( 6) SS BOND : angle 0.63680 ( 12) hydrogen bonds : bond 0.03821 ( 910) hydrogen bonds : angle 3.36107 ( 2324) link_NAG-ASN : bond 0.00571 ( 2) link_NAG-ASN : angle 3.82022 ( 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 199 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 57 SER cc_start: 0.9137 (p) cc_final: 0.8871 (p) REVERT: A 59 GLU cc_start: 0.7785 (pt0) cc_final: 0.7279 (pm20) REVERT: B 92 ARG cc_start: 0.8728 (ttp80) cc_final: 0.8374 (ttp80) REVERT: D 79 HIS cc_start: 0.8128 (t-90) cc_final: 0.7755 (t-170) REVERT: D 83 ARG cc_start: 0.7599 (mmt90) cc_final: 0.7319 (mtp-110) REVERT: E 71 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8152 (t) REVERT: G 95 LYS cc_start: 0.8570 (tttt) cc_final: 0.8369 (tttm) REVERT: L 202 GLU cc_start: 0.7698 (tp30) cc_final: 0.7473 (tp30) REVERT: L 345 SER cc_start: 0.8806 (m) cc_final: 0.8416 (t) REVERT: L 409 MET cc_start: 0.7764 (mtp) cc_final: 0.7563 (mtt) REVERT: L 530 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8355 (p) outliers start: 36 outliers final: 15 residues processed: 191 average time/residue: 0.1578 time to fit residues: 43.8643 Evaluate side-chains 168 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 71 VAL 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 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 430 LEU Chi-restraints excluded: chain L residue 530 VAL 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: 3.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN L 299 ASN L 372 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.180276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137609 restraints weight = 21576.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.140980 restraints weight = 12543.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143165 restraints weight = 9217.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144285 restraints weight = 7815.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145018 restraints weight = 7193.346| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17514 Z= 0.189 Angle : 0.562 8.329 24941 Z= 0.319 Chirality : 0.036 0.216 2803 Planarity : 0.004 0.037 2189 Dihedral : 28.426 169.634 4704 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.50 % Allowed : 24.51 % Favored : 70.99 % 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 aren not related in a simple way. whole: 2.14 (0.24), residues: 1315 helix: 2.53 (0.19), residues: 743 sheet: None (None), residues: 0 loop : -0.06 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.032 0.002 TYR D 80 PHE 0.012 0.001 PHE L 252 TRP 0.007 0.001 TRP L 602 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00441 (17506) covalent geometry : angle 0.55865 (24923) SS BOND : bond 0.00311 ( 6) SS BOND : angle 0.73468 ( 12) hydrogen bonds : bond 0.04154 ( 910) hydrogen bonds : angle 3.40114 ( 2324) link_NAG-ASN : bond 0.00393 ( 2) link_NAG-ASN : angle 4.08596 ( 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 213 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: D 79 HIS cc_start: 0.8270 (t-90) cc_final: 0.7937 (t-170) REVERT: D 83 ARG cc_start: 0.7704 (mmt90) cc_final: 0.7381 (mtm-85) REVERT: E 71 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8279 (t) REVERT: F 92 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8405 (ttp80) REVERT: G 38 ASN cc_start: 0.8204 (m-40) cc_final: 0.7957 (m110) REVERT: G 95 LYS cc_start: 0.8557 (tttt) cc_final: 0.8342 (tttm) REVERT: G 104 GLN cc_start: 0.8790 (mt0) cc_final: 0.8559 (mt0) REVERT: H 32 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7750 (mt-10) REVERT: L 202 GLU cc_start: 0.7695 (tp30) cc_final: 0.7407 (tp30) REVERT: L 248 ARG cc_start: 0.8740 (mmt-90) cc_final: 0.8539 (mmt-90) REVERT: L 345 SER cc_start: 0.8727 (m) cc_final: 0.8352 (t) REVERT: L 409 MET cc_start: 0.7789 (mtp) cc_final: 0.7555 (mtm) REVERT: L 437 TRP cc_start: 0.7860 (OUTLIER) cc_final: 0.7422 (m-10) REVERT: L 484 ASP cc_start: 0.7318 (p0) cc_final: 0.7117 (p0) REVERT: L 530 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8434 (p) REVERT: L 726 ASP cc_start: 0.7988 (p0) cc_final: 0.7405 (p0) outliers start: 51 outliers final: 31 residues processed: 204 average time/residue: 0.1421 time to fit residues: 42.7180 Evaluate side-chains 190 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 47 SER Chi-restraints excluded: chain C residue 63 LEU 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 49 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 286 VAL 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 458 THR Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 495 THR Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 588 MET Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain L residue 619 THR Chi-restraints excluded: chain L residue 703 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 49 optimal weight: 0.2980 chunk 74 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 114 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS L 299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.172771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129346 restraints weight = 21583.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132481 restraints weight = 12901.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.134288 restraints weight = 9646.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135644 restraints weight = 8297.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136227 restraints weight = 7630.412| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 17514 Z= 0.327 Angle : 0.695 9.015 24941 Z= 0.385 Chirality : 0.042 0.246 2803 Planarity : 0.005 0.039 2189 Dihedral : 28.752 169.475 4704 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.38 % Allowed : 25.49 % Favored : 69.14 % 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 aren not related in a simple way. whole: 1.48 (0.24), residues: 1315 helix: 1.99 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -0.34 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.039 0.003 TYR D 80 PHE 0.017 0.002 PHE L 252 TRP 0.006 0.001 TRP L 602 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00778 (17506) covalent geometry : angle 0.69115 (24923) SS BOND : bond 0.00394 ( 6) SS BOND : angle 0.81425 ( 12) hydrogen bonds : bond 0.05133 ( 910) hydrogen bonds : angle 3.78175 ( 2324) link_NAG-ASN : bond 0.00292 ( 2) link_NAG-ASN : angle 4.46308 ( 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 226 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 165 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8101 (pt0) cc_final: 0.7680 (pm20) REVERT: D 83 ARG cc_start: 0.7910 (mmt90) cc_final: 0.7560 (mtm-85) REVERT: E 71 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8317 (t) REVERT: G 38 ASN cc_start: 0.8546 (m-40) cc_final: 0.8318 (m-40) REVERT: G 95 LYS cc_start: 0.8604 (tttt) cc_final: 0.8386 (tttm) REVERT: G 104 GLN cc_start: 0.8950 (mt0) cc_final: 0.8674 (mt0) REVERT: H 32 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7920 (mt-10) REVERT: L 202 GLU cc_start: 0.7914 (tp30) cc_final: 0.7656 (tp30) REVERT: L 409 MET cc_start: 0.7902 (mtp) cc_final: 0.7568 (mtm) REVERT: L 437 TRP cc_start: 0.7811 (OUTLIER) cc_final: 0.7378 (m-10) REVERT: L 530 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8404 (p) REVERT: L 696 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8145 (tp40) outliers start: 61 outliers final: 44 residues processed: 217 average time/residue: 0.1488 time to fit residues: 47.2003 Evaluate side-chains 202 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 85 THR 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 109 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 49 THR 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 235 VAL Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 261 HIS Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 299 ASN 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 389 LEU Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 458 THR Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 493 VAL Chi-restraints excluded: chain L residue 495 THR Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 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 696 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 34 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** L 575 GLN ** 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 = 0.4133 r_free = 0.4133 target = 0.180450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137996 restraints weight = 21271.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141458 restraints weight = 12356.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143671 restraints weight = 9088.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144820 restraints weight = 7696.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145606 restraints weight = 7097.745| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1860 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= 0.145 Angle : 0.536 7.885 24941 Z= 0.306 Chirality : 0.034 0.184 2803 Planarity : 0.004 0.035 2189 Dihedral : 28.391 169.547 4704 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.35 % Allowed : 27.60 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.24), residues: 1315 helix: 2.49 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -0.23 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.048 0.002 TYR D 80 PHE 0.013 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 covalent geometry : bond 0.00324 (17506) covalent geometry : angle 0.53321 (24923) SS BOND : bond 0.00293 ( 6) SS BOND : angle 0.58333 ( 12) hydrogen bonds : bond 0.03709 ( 910) hydrogen bonds : angle 3.26335 ( 2324) link_NAG-ASN : bond 0.00503 ( 2) link_NAG-ASN : angle 3.83790 ( 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 199 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7891 (pt0) cc_final: 0.7392 (pm20) REVERT: D 79 HIS cc_start: 0.8267 (t-90) cc_final: 0.7956 (t-170) REVERT: D 83 ARG cc_start: 0.7729 (mmt90) cc_final: 0.7499 (mtm-85) REVERT: G 38 ASN cc_start: 0.8250 (m-40) cc_final: 0.7973 (m-40) REVERT: G 95 LYS cc_start: 0.8559 (tttt) cc_final: 0.8311 (tttm) REVERT: H 32 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7772 (mt-10) REVERT: L 202 GLU cc_start: 0.7651 (tp30) cc_final: 0.7423 (tp30) REVERT: L 345 SER cc_start: 0.8706 (m) cc_final: 0.8302 (t) REVERT: L 409 MET cc_start: 0.7781 (mtp) cc_final: 0.7495 (mtm) REVERT: L 422 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8173 (tm-30) REVERT: L 530 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8517 (p) REVERT: L 696 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7920 (tp40) REVERT: L 726 ASP cc_start: 0.8070 (p0) cc_final: 0.7851 (p0) outliers start: 38 outliers final: 18 residues processed: 189 average time/residue: 0.1374 time to fit residues: 38.5551 Evaluate side-chains 174 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 87 THR 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 100 VAL 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 326 ILE Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 563 ILE Chi-restraints excluded: chain L residue 588 MET Chi-restraints excluded: chain L residue 654 LYS Chi-restraints excluded: chain L residue 696 GLN Chi-restraints excluded: chain L residue 717 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 116 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.0870 chunk 36 optimal weight: 0.8980 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 299 ASN L 575 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.179258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.136639 restraints weight = 21435.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140044 restraints weight = 12529.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.142213 restraints weight = 9169.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143460 restraints weight = 7799.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144065 restraints weight = 7160.330| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17514 Z= 0.167 Angle : 0.555 8.064 24941 Z= 0.313 Chirality : 0.035 0.193 2803 Planarity : 0.004 0.037 2189 Dihedral : 28.429 169.493 4703 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.53 % Allowed : 27.43 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.24), residues: 1315 helix: 2.51 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -0.19 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 92 TYR 0.049 0.002 TYR D 80 PHE 0.011 0.001 PHE E 67 TRP 0.008 0.001 TRP L 602 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00387 (17506) covalent geometry : angle 0.55141 (24923) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.60780 ( 12) hydrogen bonds : bond 0.03863 ( 910) hydrogen bonds : angle 3.29765 ( 2324) link_NAG-ASN : bond 0.00446 ( 2) link_NAG-ASN : angle 3.96262 ( 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 197 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7832 (pt0) cc_final: 0.7441 (pm20) REVERT: D 56 MET cc_start: 0.8434 (tpp) cc_final: 0.8221 (tpp) REVERT: D 79 HIS cc_start: 0.8267 (t-90) cc_final: 0.7988 (t-170) REVERT: D 83 ARG cc_start: 0.7761 (mmt90) cc_final: 0.7530 (mtm-85) REVERT: F 77 LYS cc_start: 0.8929 (mttm) cc_final: 0.8722 (tppp) REVERT: G 38 ASN cc_start: 0.8223 (m-40) cc_final: 0.7960 (m-40) REVERT: G 95 LYS cc_start: 0.8559 (tttt) cc_final: 0.8340 (tttm) REVERT: G 104 GLN cc_start: 0.8765 (mt0) cc_final: 0.8547 (mt0) REVERT: L 202 GLU cc_start: 0.7687 (tp30) cc_final: 0.7481 (tp30) REVERT: L 345 SER cc_start: 0.8653 (m) cc_final: 0.8279 (t) REVERT: L 422 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8167 (tm-30) REVERT: L 437 TRP cc_start: 0.7819 (OUTLIER) cc_final: 0.7410 (m-10) REVERT: L 726 ASP cc_start: 0.8185 (p0) cc_final: 0.7928 (p0) outliers start: 40 outliers final: 28 residues processed: 189 average time/residue: 0.1393 time to fit residues: 38.7621 Evaluate side-chains 183 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 87 THR 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 100 VAL Chi-restraints excluded: chain H residue 64 ASN 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 299 ASN Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain L residue 326 ILE 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 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 688 MET Chi-restraints excluded: chain L residue 717 ILE Chi-restraints excluded: chain L residue 722 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.176873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.133946 restraints weight = 21326.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.137156 restraints weight = 12610.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.139282 restraints weight = 9366.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140517 restraints weight = 7977.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.140974 restraints weight = 7325.174| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17514 Z= 0.217 Angle : 0.593 8.247 24941 Z= 0.332 Chirality : 0.037 0.234 2803 Planarity : 0.004 0.035 2189 Dihedral : 28.514 169.552 4702 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.88 % Allowed : 27.34 % 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 aren not related in a simple way. whole: 1.81 (0.24), residues: 1315 helix: 2.29 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.28 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 92 TYR 0.056 0.002 TYR D 80 PHE 0.010 0.001 PHE E 67 TRP 0.007 0.001 TRP L 602 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00511 (17506) covalent geometry : angle 0.58980 (24923) SS BOND : bond 0.00323 ( 6) SS BOND : angle 0.62626 ( 12) hydrogen bonds : bond 0.04219 ( 910) hydrogen bonds : angle 3.42877 ( 2324) link_NAG-ASN : bond 0.00397 ( 2) link_NAG-ASN : angle 4.03996 ( 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 200 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7864 (pt0) cc_final: 0.7484 (pm20) REVERT: D 28 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7408 (mtmm) REVERT: D 79 HIS cc_start: 0.8289 (t-90) cc_final: 0.8027 (t-170) REVERT: E 71 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8354 (t) REVERT: G 38 ASN cc_start: 0.8296 (m-40) cc_final: 0.8033 (m-40) REVERT: G 90 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7463 (t0) REVERT: G 104 GLN cc_start: 0.8780 (mt0) cc_final: 0.8573 (mt0) REVERT: H 32 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7763 (mt-10) REVERT: L 345 SER cc_start: 0.8630 (m) cc_final: 0.8273 (t) REVERT: L 422 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8106 (tm-30) REVERT: L 437 TRP cc_start: 0.7791 (OUTLIER) cc_final: 0.7367 (m-10) REVERT: L 566 ASP cc_start: 0.8033 (p0) cc_final: 0.7725 (t70) REVERT: L 726 ASP cc_start: 0.8205 (p0) cc_final: 0.7943 (p0) outliers start: 44 outliers final: 33 residues processed: 191 average time/residue: 0.1350 time to fit residues: 38.0297 Evaluate side-chains 188 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 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 B residue 49 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 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 90 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 64 ASN 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 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 430 LEU Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 458 THR Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 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 688 MET Chi-restraints excluded: chain L residue 711 THR Chi-restraints excluded: chain L residue 717 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 13 optimal weight: 0.9990 chunk 120 optimal weight: 0.0170 chunk 9 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 60 optimal weight: 0.0770 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.184173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142153 restraints weight = 21395.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145652 restraints weight = 12285.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147903 restraints weight = 8981.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148767 restraints weight = 7597.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.149795 restraints weight = 7050.113| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17514 Z= 0.130 Angle : 0.529 8.688 24941 Z= 0.300 Chirality : 0.034 0.186 2803 Planarity : 0.004 0.037 2189 Dihedral : 28.227 169.828 4702 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.65 % Allowed : 28.84 % Favored : 68.52 % 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 aren not related in a simple way. whole: 2.14 (0.24), residues: 1315 helix: 2.55 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.13 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 92 TYR 0.054 0.002 TYR D 80 PHE 0.012 0.001 PHE A 67 TRP 0.012 0.001 TRP L 602 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00282 (17506) covalent geometry : angle 0.52628 (24923) SS BOND : bond 0.00287 ( 6) SS BOND : angle 0.56349 ( 12) hydrogen bonds : bond 0.03520 ( 910) hydrogen bonds : angle 3.16593 ( 2324) link_NAG-ASN : bond 0.00578 ( 2) link_NAG-ASN : angle 3.77037 ( 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 184 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7827 (pt0) cc_final: 0.7386 (pm20) REVERT: D 56 MET cc_start: 0.8431 (tpp) cc_final: 0.8083 (tpp) REVERT: E 71 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8189 (t) REVERT: F 77 LYS cc_start: 0.8961 (mttm) cc_final: 0.8746 (tppp) REVERT: L 345 SER cc_start: 0.8576 (m) cc_final: 0.8198 (t) REVERT: L 437 TRP cc_start: 0.7714 (OUTLIER) cc_final: 0.7420 (m-10) REVERT: L 517 GLN cc_start: 0.8091 (mm110) cc_final: 0.7888 (mm-40) REVERT: L 566 ASP cc_start: 0.7903 (p0) cc_final: 0.7699 (t70) REVERT: L 631 MET cc_start: 0.8311 (mmp) cc_final: 0.7987 (mmt) REVERT: L 726 ASP cc_start: 0.8196 (p0) cc_final: 0.7653 (p0) outliers start: 30 outliers final: 21 residues processed: 177 average time/residue: 0.1283 time to fit residues: 33.6865 Evaluate side-chains 168 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR 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 71 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 87 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 308 ASP Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 563 ILE Chi-restraints excluded: chain L residue 588 MET Chi-restraints excluded: chain L residue 654 LYS Chi-restraints excluded: chain L residue 688 MET Chi-restraints excluded: chain L residue 717 ILE Chi-restraints excluded: chain L residue 722 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 79 HIS E 93 GLN G 38 ASN L 257 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.182674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.140293 restraints weight = 21446.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143665 restraints weight = 12380.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145872 restraints weight = 9134.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147143 restraints weight = 7730.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147894 restraints weight = 7072.397| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17514 Z= 0.144 Angle : 0.538 8.655 24941 Z= 0.303 Chirality : 0.034 0.189 2803 Planarity : 0.004 0.080 2189 Dihedral : 28.292 169.619 4702 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.73 % Allowed : 28.92 % Favored : 68.34 % 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 aren not related in a simple way. whole: 2.18 (0.24), residues: 1315 helix: 2.59 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.12 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.030 0.001 TYR D 80 PHE 0.011 0.001 PHE A 67 TRP 0.009 0.001 TRP L 602 HIS 0.010 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00324 (17506) covalent geometry : angle 0.53438 (24923) SS BOND : bond 0.00272 ( 6) SS BOND : angle 0.56726 ( 12) hydrogen bonds : bond 0.03668 ( 910) hydrogen bonds : angle 3.16693 ( 2324) link_NAG-ASN : bond 0.00482 ( 2) link_NAG-ASN : angle 3.85161 ( 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 183 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7807 (pt0) cc_final: 0.7416 (pm20) REVERT: D 28 LYS cc_start: 0.7760 (mtmm) cc_final: 0.7469 (mtmm) REVERT: E 71 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8284 (t) REVERT: F 92 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8553 (ttp80) REVERT: L 345 SER cc_start: 0.8616 (m) cc_final: 0.8242 (t) REVERT: L 437 TRP cc_start: 0.7795 (OUTLIER) cc_final: 0.7450 (m-10) REVERT: L 517 GLN cc_start: 0.8000 (mm110) cc_final: 0.7781 (mm-40) REVERT: L 631 MET cc_start: 0.8385 (mmp) cc_final: 0.7976 (mmt) REVERT: L 726 ASP cc_start: 0.8207 (p0) cc_final: 0.7743 (p0) outliers start: 31 outliers final: 24 residues processed: 176 average time/residue: 0.1332 time to fit residues: 34.9065 Evaluate side-chains 171 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 16 THR Chi-restraints excluded: chain C residue 79 ILE 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 71 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 87 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 308 ASP Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 563 ILE 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 722 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 86 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.181907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.139413 restraints weight = 21457.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142789 restraints weight = 12479.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144980 restraints weight = 9165.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.146073 restraints weight = 7778.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146879 restraints weight = 7172.782| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17514 Z= 0.156 Angle : 0.548 8.574 24941 Z= 0.308 Chirality : 0.035 0.194 2803 Planarity : 0.004 0.056 2189 Dihedral : 28.309 169.663 4702 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.47 % Allowed : 29.10 % Favored : 68.43 % 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 aren not related in a simple way. whole: 2.14 (0.24), residues: 1315 helix: 2.56 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -0.12 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 92 TYR 0.031 0.002 TYR D 37 PHE 0.010 0.001 PHE A 67 TRP 0.008 0.001 TRP L 602 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00357 (17506) covalent geometry : angle 0.54457 (24923) SS BOND : bond 0.00271 ( 6) SS BOND : angle 0.52560 ( 12) hydrogen bonds : bond 0.03763 ( 910) hydrogen bonds : angle 3.21500 ( 2324) link_NAG-ASN : bond 0.00487 ( 2) link_NAG-ASN : angle 3.86500 ( 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 178 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7835 (pt0) cc_final: 0.7433 (pm20) REVERT: D 28 LYS cc_start: 0.7646 (mtmm) cc_final: 0.7404 (mtmm) REVERT: E 71 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8307 (t) REVERT: F 92 ARG cc_start: 0.8823 (ttp80) cc_final: 0.8546 (ttp80) REVERT: L 345 SER cc_start: 0.8578 (m) cc_final: 0.8235 (t) REVERT: L 437 TRP cc_start: 0.7802 (OUTLIER) cc_final: 0.7463 (m-10) REVERT: L 726 ASP cc_start: 0.8153 (p0) cc_final: 0.7636 (p0) outliers start: 28 outliers final: 25 residues processed: 173 average time/residue: 0.1377 time to fit residues: 35.2008 Evaluate side-chains 171 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 16 THR Chi-restraints excluded: chain C residue 79 ILE 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 71 VAL 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 100 VAL Chi-restraints excluded: chain H residue 87 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 308 ASP Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 563 ILE 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 722 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 19 optimal weight: 0.4980 chunk 145 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 137 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.180450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.137805 restraints weight = 21403.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.141165 restraints weight = 12428.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143342 restraints weight = 9189.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144571 restraints weight = 7813.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145030 restraints weight = 7177.335| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17514 Z= 0.173 Angle : 0.563 8.327 24941 Z= 0.315 Chirality : 0.035 0.199 2803 Planarity : 0.004 0.055 2189 Dihedral : 28.369 169.651 4702 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.65 % Allowed : 29.10 % Favored : 68.25 % 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 aren not related in a simple way. whole: 2.08 (0.24), residues: 1315 helix: 2.50 (0.19), residues: 745 sheet: None (None), residues: 0 loop : -0.13 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 92 TYR 0.034 0.002 TYR D 37 PHE 0.011 0.001 PHE L 531 TRP 0.007 0.001 TRP L 602 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00401 (17506) covalent geometry : angle 0.55979 (24923) SS BOND : bond 0.00287 ( 6) SS BOND : angle 0.53942 ( 12) hydrogen bonds : bond 0.03885 ( 910) hydrogen bonds : angle 3.27303 ( 2324) link_NAG-ASN : bond 0.00446 ( 2) link_NAG-ASN : angle 3.91787 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.05 seconds wall clock time: 40 minutes 22.62 seconds (2422.62 seconds total)