Starting phenix.real_space_refine on Wed Feb 4 08:54:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kb7_62219/02_2026/9kb7_62219.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kb7_62219/02_2026/9kb7_62219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kb7_62219/02_2026/9kb7_62219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kb7_62219/02_2026/9kb7_62219.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kb7_62219/02_2026/9kb7_62219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kb7_62219/02_2026/9kb7_62219.map" } resolution = 3.97 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3495 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 4319 2.51 5 N 1121 2.21 5 O 1217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6706 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5880 Classifications: {'peptide': 754} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 715} Chain breaks: 1 Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 826 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Time building chain proxies: 1.60, per 1000 atoms: 0.24 Number of scatterers: 6706 At special positions: 0 Unit cell: (74.7, 84.0375, 157.181, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1217 8.00 N 1121 7.00 C 4319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 35 " distance=2.03 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 46 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 141 " 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 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 260.6 milliseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1616 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 11 sheets defined 33.9% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.038A pdb=" N PHE A 385 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 466 through 472 removed outlier: 3.972A pdb=" N ALA A 472 " --> pdb=" O GLN A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 565 removed outlier: 3.643A pdb=" N THR A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 removed outlier: 3.546A pdb=" N ILE A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 588 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 4.310A pdb=" N PHE A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TRP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 653 removed outlier: 3.893A pdb=" N LYS A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU A 638 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 683 removed outlier: 3.534A pdb=" N LEU A 667 " --> pdb=" O ARG A 663 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 668 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) Proline residue: A 680 - end of helix removed outlier: 3.722A pdb=" N HIS A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 690 removed outlier: 3.634A pdb=" N ALA A 689 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 690 " --> pdb=" O TYR A 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 686 through 690' Processing helix chain 'A' and resid 700 through 732 removed outlier: 3.638A pdb=" N VAL A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA A 722 " --> pdb=" O PHE A 718 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR A 725 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 Processing helix chain 'A' and resid 740 through 759 removed outlier: 4.197A pdb=" N SER A 744 " --> pdb=" O ASN A 740 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP A 751 " --> pdb=" O LYS A 747 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 752 " --> pdb=" O HIS A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 768 removed outlier: 4.594A pdb=" N VAL A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 790 removed outlier: 3.752A pdb=" N THR A 786 " --> pdb=" O MET A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 804 removed outlier: 3.910A pdb=" N CYS A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Proline residue: A 798 - end of helix removed outlier: 3.836A pdb=" N TYR A 801 " --> pdb=" O ASN A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 822 removed outlier: 3.999A pdb=" N LYS A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 810 " --> pdb=" O PRO A 806 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 37 removed outlier: 4.769A pdb=" N CYS A 35 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP A 42 " --> pdb=" O CYS A 35 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU A 134 " --> pdb=" O TRP A 159 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU A 158 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU A 182 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.559A pdb=" N ILE A 192 " --> pdb=" O SER A 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 303 Processing sheet with id=AA6, first strand: chain 'A' and resid 379 through 380 removed outlier: 3.553A pdb=" N ILE A 380 " --> pdb=" O GLU A 403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 46 removed outlier: 6.659A pdb=" N CYS B 43 " --> pdb=" O CYS B 55 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS B 55 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER B 45 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.636A pdb=" N PHE B 60 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU B 63 " --> pdb=" O CYS B 93 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N ARG B 95 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 14.516A pdb=" N ARG B 65 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 92 " --> pdb=" O HIS B 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 101 through 104 removed outlier: 3.606A pdb=" N SER B 103 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 118 through 120 Processing sheet with id=AB2, first strand: chain 'B' and resid 133 through 135 231 hydrogen bonds defined for protein. 636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1532 1.33 - 1.45: 1421 1.45 - 1.57: 3850 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 6865 Sorted by residual: bond pdb=" N LEU A 694 " pdb=" CA LEU A 694 " ideal model delta sigma weight residual 1.463 1.486 -0.023 8.80e-03 1.29e+04 6.94e+00 bond pdb=" N THR A 701 " pdb=" CA THR A 701 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.41e-02 5.03e+03 6.60e+00 bond pdb=" N GLU A 700 " pdb=" CA GLU A 700 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.25e-02 6.40e+03 6.14e+00 bond pdb=" N THR A 698 " pdb=" CA THR A 698 " ideal model delta sigma weight residual 1.457 1.487 -0.031 1.31e-02 5.83e+03 5.46e+00 bond pdb=" N LEU A 704 " pdb=" CA LEU A 704 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.17e-02 7.31e+03 5.31e+00 ... (remaining 6860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 9150 2.26 - 4.52: 126 4.52 - 6.78: 19 6.78 - 9.04: 11 9.04 - 11.30: 4 Bond angle restraints: 9310 Sorted by residual: angle pdb=" N GLU A 84 " pdb=" CA GLU A 84 " pdb=" C GLU A 84 " ideal model delta sigma weight residual 114.75 104.36 10.39 1.26e+00 6.30e-01 6.81e+01 angle pdb=" N LEU A 692 " pdb=" CA LEU A 692 " pdb=" C LEU A 692 " ideal model delta sigma weight residual 112.54 107.23 5.31 1.22e+00 6.72e-01 1.89e+01 angle pdb=" CB MET B 90 " pdb=" CG MET B 90 " pdb=" SD MET B 90 " ideal model delta sigma weight residual 112.70 124.00 -11.30 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CB MET A 540 " pdb=" CG MET A 540 " pdb=" SD MET A 540 " ideal model delta sigma weight residual 112.70 122.70 -10.00 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA GLU A 700 " pdb=" C GLU A 700 " pdb=" O GLU A 700 " ideal model delta sigma weight residual 120.66 116.85 3.81 1.15e+00 7.56e-01 1.10e+01 ... (remaining 9305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 3525 15.74 - 31.48: 458 31.48 - 47.22: 122 47.22 - 62.96: 28 62.96 - 78.70: 7 Dihedral angle restraints: 4140 sinusoidal: 1653 harmonic: 2487 Sorted by residual: dihedral pdb=" CB CYS B 78 " pdb=" SG CYS B 78 " pdb=" SG CYS B 93 " pdb=" CB CYS B 93 " ideal model delta sinusoidal sigma weight residual -86.00 -138.55 52.55 1 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" CB CYS A 29 " pdb=" SG CYS A 29 " pdb=" SG CYS A 35 " pdb=" CB CYS A 35 " ideal model delta sinusoidal sigma weight residual 93.00 40.54 52.46 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS A 618 " pdb=" SG CYS A 618 " pdb=" SG CYS A 693 " pdb=" CB CYS A 693 " ideal model delta sinusoidal sigma weight residual -86.00 -127.29 41.29 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 4137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 734 0.039 - 0.078: 246 0.078 - 0.118: 71 0.118 - 0.157: 10 0.157 - 0.196: 4 Chirality restraints: 1065 Sorted by residual: chirality pdb=" CA GLU B 140 " pdb=" N GLU B 140 " pdb=" C GLU B 140 " pdb=" CB GLU B 140 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CG LEU A 710 " pdb=" CB LEU A 710 " pdb=" CD1 LEU A 710 " pdb=" CD2 LEU A 710 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA GLU A 84 " pdb=" N GLU A 84 " pdb=" C GLU A 84 " pdb=" CB GLU A 84 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 1062 not shown) Planarity restraints: 1187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 97 " -0.356 9.50e-02 1.11e+02 1.59e-01 1.56e+01 pdb=" NE ARG B 97 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 97 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 97 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 97 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 83 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C LEU A 83 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU A 83 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU A 84 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 139 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C MET B 139 " -0.027 2.00e-02 2.50e+03 pdb=" O MET B 139 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU B 140 " 0.009 2.00e-02 2.50e+03 ... (remaining 1184 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 169 2.67 - 3.23: 6873 3.23 - 3.78: 11183 3.78 - 4.34: 14276 4.34 - 4.90: 22724 Nonbonded interactions: 55225 Sorted by model distance: nonbonded pdb=" OH TYR A 725 " pdb=" O ILE A 746 " model vdw 2.110 3.040 nonbonded pdb=" O MET A 637 " pdb=" OG1 THR A 640 " model vdw 2.198 3.040 nonbonded pdb=" O SER A 583 " pdb=" OG SER A 628 " model vdw 2.232 3.040 nonbonded pdb=" O ASP A 75 " pdb=" NZ LYS A 78 " model vdw 2.254 3.120 nonbonded pdb=" O VAL A 559 " pdb=" OG1 THR A 562 " model vdw 2.256 3.040 ... (remaining 55220 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 0.038 6879 Z= 0.176 Angle : 0.699 11.303 9338 Z= 0.350 Chirality : 0.043 0.196 1065 Planarity : 0.005 0.159 1187 Dihedral : 15.153 78.701 2482 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.93 % Favored : 96.71 % Rotamer: Outliers : 0.66 % Allowed : 25.70 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.31), residues: 852 helix: 0.48 (0.35), residues: 231 sheet: -1.39 (0.50), residues: 127 loop : 0.03 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 542 TYR 0.005 0.001 TYR A 466 PHE 0.025 0.001 PHE A 547 TRP 0.008 0.001 TRP A 546 HIS 0.002 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6865) covalent geometry : angle 0.69914 ( 9310) SS BOND : bond 0.00160 ( 14) SS BOND : angle 0.49187 ( 28) hydrogen bonds : bond 0.28723 ( 231) hydrogen bonds : angle 8.83145 ( 636) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 694 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9024 (mt) REVERT: A 714 ASN cc_start: 0.9135 (m-40) cc_final: 0.8688 (t0) outliers start: 5 outliers final: 3 residues processed: 84 average time/residue: 0.0502 time to fit residues: 6.2433 Evaluate side-chains 83 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain B residue 97 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 658 HIS A 714 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.061840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.046742 restraints weight = 32086.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.048364 restraints weight = 18463.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.049485 restraints weight = 12680.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.050283 restraints weight = 9729.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.050791 restraints weight = 8046.788| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6879 Z= 0.121 Angle : 0.641 10.000 9338 Z= 0.305 Chirality : 0.044 0.315 1065 Planarity : 0.003 0.029 1187 Dihedral : 5.191 57.963 912 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 1.99 % Allowed : 22.25 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.30), residues: 852 helix: 1.09 (0.34), residues: 235 sheet: -1.12 (0.51), residues: 122 loop : -0.07 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.006 0.001 TYR A 466 PHE 0.018 0.001 PHE A 696 TRP 0.006 0.001 TRP A 539 HIS 0.002 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6865) covalent geometry : angle 0.64142 ( 9310) SS BOND : bond 0.00181 ( 14) SS BOND : angle 0.42730 ( 28) hydrogen bonds : bond 0.05130 ( 231) hydrogen bonds : angle 5.25823 ( 636) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.9221 (tpp) cc_final: 0.8629 (mmm) REVERT: A 634 PHE cc_start: 0.8882 (m-80) cc_final: 0.8681 (m-80) REVERT: A 671 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9323 (pp) REVERT: A 745 MET cc_start: 0.9159 (mmm) cc_final: 0.8934 (mmm) REVERT: A 756 ASN cc_start: 0.9338 (m-40) cc_final: 0.8806 (m110) REVERT: A 787 LEU cc_start: 0.9705 (mt) cc_final: 0.9484 (mt) REVERT: A 790 PHE cc_start: 0.9457 (t80) cc_final: 0.9204 (t80) REVERT: A 795 CYS cc_start: 0.8937 (p) cc_final: 0.8613 (p) outliers start: 15 outliers final: 3 residues processed: 102 average time/residue: 0.0493 time to fit residues: 7.3985 Evaluate side-chains 87 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 692 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.061010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.045823 restraints weight = 32482.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.047432 restraints weight = 18832.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.048501 restraints weight = 12974.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.049323 restraints weight = 10029.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.049852 restraints weight = 8284.911| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6879 Z= 0.143 Angle : 0.636 10.152 9338 Z= 0.298 Chirality : 0.042 0.284 1065 Planarity : 0.003 0.034 1187 Dihedral : 4.018 40.974 905 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 3.05 % Allowed : 21.72 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.31), residues: 852 helix: 1.34 (0.34), residues: 235 sheet: -1.23 (0.49), residues: 123 loop : -0.06 (0.31), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 97 TYR 0.007 0.001 TYR A 466 PHE 0.012 0.001 PHE A 696 TRP 0.005 0.001 TRP A 159 HIS 0.002 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6865) covalent geometry : angle 0.63654 ( 9310) SS BOND : bond 0.00205 ( 14) SS BOND : angle 0.46136 ( 28) hydrogen bonds : bond 0.04355 ( 231) hydrogen bonds : angle 4.89749 ( 636) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 587 MET cc_start: 0.9262 (tpp) cc_final: 0.8856 (tpp) REVERT: A 637 MET cc_start: 0.9438 (ppp) cc_final: 0.8746 (pmm) REVERT: A 671 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9304 (pp) REVERT: A 756 ASN cc_start: 0.9356 (m-40) cc_final: 0.8806 (m110) REVERT: B 108 ASP cc_start: 0.9190 (p0) cc_final: 0.8957 (p0) outliers start: 23 outliers final: 10 residues processed: 98 average time/residue: 0.0523 time to fit residues: 7.5686 Evaluate side-chains 91 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 84 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.060345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.045303 restraints weight = 33557.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.046822 restraints weight = 19785.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.047842 restraints weight = 13842.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.048609 restraints weight = 10837.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.049130 restraints weight = 9034.857| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6879 Z= 0.194 Angle : 0.663 10.000 9338 Z= 0.315 Chirality : 0.044 0.330 1065 Planarity : 0.003 0.030 1187 Dihedral : 4.164 37.316 905 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.77 % Rotamer: Outliers : 3.05 % Allowed : 22.78 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.31), residues: 852 helix: 1.17 (0.34), residues: 241 sheet: -1.35 (0.48), residues: 124 loop : -0.17 (0.31), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 97 TYR 0.007 0.001 TYR A 466 PHE 0.019 0.001 PHE A 790 TRP 0.008 0.001 TRP A 546 HIS 0.003 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 6865) covalent geometry : angle 0.66291 ( 9310) SS BOND : bond 0.00269 ( 14) SS BOND : angle 0.51261 ( 28) hydrogen bonds : bond 0.04052 ( 231) hydrogen bonds : angle 4.88834 ( 636) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.9320 (tpp) cc_final: 0.9006 (tpp) REVERT: A 634 PHE cc_start: 0.8902 (m-80) cc_final: 0.8652 (m-80) REVERT: A 671 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9286 (pp) outliers start: 23 outliers final: 16 residues processed: 94 average time/residue: 0.0485 time to fit residues: 6.7000 Evaluate side-chains 94 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.060163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.044954 restraints weight = 33215.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.046494 restraints weight = 19396.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.047520 restraints weight = 13482.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.048316 restraints weight = 10566.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.048878 restraints weight = 8739.631| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6879 Z= 0.153 Angle : 0.637 11.889 9338 Z= 0.299 Chirality : 0.043 0.350 1065 Planarity : 0.003 0.030 1187 Dihedral : 4.042 31.777 905 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 3.31 % Allowed : 23.71 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.31), residues: 852 helix: 1.18 (0.34), residues: 241 sheet: -1.36 (0.49), residues: 124 loop : -0.19 (0.31), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.007 0.001 TYR B 118 PHE 0.014 0.001 PHE A 790 TRP 0.006 0.001 TRP A 159 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6865) covalent geometry : angle 0.63711 ( 9310) SS BOND : bond 0.00240 ( 14) SS BOND : angle 0.47290 ( 28) hydrogen bonds : bond 0.03794 ( 231) hydrogen bonds : angle 4.77839 ( 636) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 671 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9281 (pp) REVERT: A 716 LEU cc_start: 0.9744 (tp) cc_final: 0.9536 (pp) outliers start: 25 outliers final: 17 residues processed: 95 average time/residue: 0.0547 time to fit residues: 7.5802 Evaluate side-chains 95 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.061331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.045936 restraints weight = 33375.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.047549 restraints weight = 19359.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.048631 restraints weight = 13408.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.049439 restraints weight = 10411.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.050040 restraints weight = 8625.407| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6879 Z= 0.120 Angle : 0.640 12.336 9338 Z= 0.296 Chirality : 0.043 0.351 1065 Planarity : 0.003 0.033 1187 Dihedral : 3.822 23.361 905 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 2.52 % Allowed : 24.64 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.31), residues: 852 helix: 1.23 (0.35), residues: 241 sheet: -1.37 (0.48), residues: 127 loop : -0.16 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.010 0.001 TYR B 118 PHE 0.012 0.001 PHE A 790 TRP 0.007 0.001 TRP A 159 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6865) covalent geometry : angle 0.64040 ( 9310) SS BOND : bond 0.00197 ( 14) SS BOND : angle 0.49419 ( 28) hydrogen bonds : bond 0.03587 ( 231) hydrogen bonds : angle 4.69148 ( 636) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.9227 (tpp) cc_final: 0.8679 (mmm) REVERT: A 671 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9284 (pp) REVERT: A 716 LEU cc_start: 0.9736 (tp) cc_final: 0.9530 (pp) REVERT: A 753 ILE cc_start: 0.9655 (pt) cc_final: 0.9356 (tt) REVERT: A 756 ASN cc_start: 0.9349 (m-40) cc_final: 0.9028 (m110) outliers start: 19 outliers final: 15 residues processed: 95 average time/residue: 0.0581 time to fit residues: 8.0749 Evaluate side-chains 94 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 16 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.0030 chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.061885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.046358 restraints weight = 32920.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.047957 restraints weight = 19217.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.049018 restraints weight = 13359.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.049822 restraints weight = 10436.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.050465 restraints weight = 8672.820| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6879 Z= 0.108 Angle : 0.656 12.630 9338 Z= 0.297 Chirality : 0.043 0.353 1065 Planarity : 0.003 0.029 1187 Dihedral : 3.575 20.619 903 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.07 % Rotamer: Outliers : 2.91 % Allowed : 24.37 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.31), residues: 852 helix: 1.15 (0.34), residues: 247 sheet: -1.26 (0.49), residues: 127 loop : -0.12 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 92 TYR 0.010 0.001 TYR B 118 PHE 0.010 0.001 PHE A 718 TRP 0.007 0.001 TRP A 159 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6865) covalent geometry : angle 0.65652 ( 9310) SS BOND : bond 0.00171 ( 14) SS BOND : angle 0.38640 ( 28) hydrogen bonds : bond 0.03421 ( 231) hydrogen bonds : angle 4.62345 ( 636) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.9331 (tpp) cc_final: 0.8730 (tpp) REVERT: A 671 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9271 (pp) REVERT: A 716 LEU cc_start: 0.9747 (tp) cc_final: 0.9537 (pp) REVERT: A 795 CYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8702 (p) outliers start: 22 outliers final: 15 residues processed: 96 average time/residue: 0.0573 time to fit residues: 8.0558 Evaluate side-chains 93 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 62 optimal weight: 0.0040 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 0.0020 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.062900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.047932 restraints weight = 33887.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.049545 restraints weight = 19519.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.050488 restraints weight = 13500.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.051353 restraints weight = 10710.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.051795 restraints weight = 8829.150| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6879 Z= 0.133 Angle : 0.689 12.677 9338 Z= 0.313 Chirality : 0.043 0.361 1065 Planarity : 0.003 0.031 1187 Dihedral : 3.703 22.111 903 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 2.52 % Allowed : 24.77 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.30), residues: 852 helix: 1.10 (0.34), residues: 247 sheet: -1.28 (0.49), residues: 127 loop : -0.17 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 817 TYR 0.006 0.001 TYR A 466 PHE 0.011 0.001 PHE A 765 TRP 0.005 0.001 TRP A 159 HIS 0.002 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6865) covalent geometry : angle 0.68896 ( 9310) SS BOND : bond 0.00189 ( 14) SS BOND : angle 0.64256 ( 28) hydrogen bonds : bond 0.03364 ( 231) hydrogen bonds : angle 4.63537 ( 636) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.9251 (tpp) cc_final: 0.8579 (tpp) REVERT: A 671 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9271 (pp) REVERT: A 716 LEU cc_start: 0.9702 (tp) cc_final: 0.9500 (pp) REVERT: A 756 ASN cc_start: 0.9444 (m-40) cc_final: 0.9230 (m110) outliers start: 19 outliers final: 16 residues processed: 90 average time/residue: 0.0558 time to fit residues: 7.3589 Evaluate side-chains 93 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 45 optimal weight: 0.0570 chunk 79 optimal weight: 1.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.064546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049410 restraints weight = 33515.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.051061 restraints weight = 19245.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.052220 restraints weight = 13251.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.053016 restraints weight = 10210.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.053449 restraints weight = 8482.960| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6879 Z= 0.102 Angle : 0.705 13.446 9338 Z= 0.311 Chirality : 0.043 0.367 1065 Planarity : 0.003 0.029 1187 Dihedral : 3.449 18.189 903 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.07 % Rotamer: Outliers : 1.99 % Allowed : 25.30 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.31), residues: 852 helix: 1.22 (0.35), residues: 242 sheet: -1.14 (0.49), residues: 126 loop : -0.12 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 92 TYR 0.007 0.001 TYR B 118 PHE 0.011 0.001 PHE B 117 TRP 0.011 0.001 TRP A 751 HIS 0.002 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6865) covalent geometry : angle 0.70401 ( 9310) SS BOND : bond 0.00164 ( 14) SS BOND : angle 0.85811 ( 28) hydrogen bonds : bond 0.03223 ( 231) hydrogen bonds : angle 4.56779 ( 636) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.9192 (tpp) cc_final: 0.8554 (tpp) REVERT: A 671 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9251 (pp) REVERT: A 716 LEU cc_start: 0.9695 (tp) cc_final: 0.9492 (pp) REVERT: A 756 ASN cc_start: 0.9393 (m-40) cc_final: 0.9164 (m110) REVERT: A 795 CYS cc_start: 0.8824 (p) cc_final: 0.8537 (p) outliers start: 15 outliers final: 12 residues processed: 92 average time/residue: 0.0519 time to fit residues: 6.8138 Evaluate side-chains 95 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain B residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.063797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048742 restraints weight = 33343.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.050359 restraints weight = 19288.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.051309 restraints weight = 13348.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.052186 restraints weight = 10646.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.052746 restraints weight = 8795.154| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6879 Z= 0.118 Angle : 0.702 13.885 9338 Z= 0.313 Chirality : 0.043 0.363 1065 Planarity : 0.003 0.031 1187 Dihedral : 3.510 18.384 903 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.58 % Favored : 97.30 % Rotamer: Outliers : 1.99 % Allowed : 25.30 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.30), residues: 852 helix: 1.10 (0.34), residues: 248 sheet: -1.15 (0.49), residues: 126 loop : -0.15 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 817 TYR 0.008 0.001 TYR B 118 PHE 0.012 0.001 PHE A 547 TRP 0.006 0.001 TRP A 751 HIS 0.002 0.000 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6865) covalent geometry : angle 0.70234 ( 9310) SS BOND : bond 0.00163 ( 14) SS BOND : angle 0.71872 ( 28) hydrogen bonds : bond 0.03187 ( 231) hydrogen bonds : angle 4.53217 ( 636) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.9222 (tpp) cc_final: 0.8536 (tpp) REVERT: A 671 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9253 (pp) REVERT: A 716 LEU cc_start: 0.9700 (tp) cc_final: 0.9499 (pp) REVERT: A 756 ASN cc_start: 0.9415 (m-40) cc_final: 0.9203 (m110) outliers start: 15 outliers final: 12 residues processed: 88 average time/residue: 0.0445 time to fit residues: 5.9407 Evaluate side-chains 90 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain B residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 2 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.062367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.047619 restraints weight = 34022.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.049177 restraints weight = 19807.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.050201 restraints weight = 13805.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.051000 restraints weight = 10776.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.051511 restraints weight = 8969.237| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6879 Z= 0.193 Angle : 0.733 13.050 9338 Z= 0.336 Chirality : 0.044 0.331 1065 Planarity : 0.003 0.031 1187 Dihedral : 3.882 18.361 903 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 1.99 % Allowed : 25.43 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.30), residues: 852 helix: 1.03 (0.34), residues: 249 sheet: -1.35 (0.48), residues: 127 loop : -0.20 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 135 TYR 0.010 0.001 TYR B 118 PHE 0.012 0.001 PHE A 547 TRP 0.010 0.001 TRP A 546 HIS 0.003 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 6865) covalent geometry : angle 0.73309 ( 9310) SS BOND : bond 0.00251 ( 14) SS BOND : angle 0.78826 ( 28) hydrogen bonds : bond 0.03551 ( 231) hydrogen bonds : angle 4.64581 ( 636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 951.76 seconds wall clock time: 17 minutes 9.80 seconds (1029.80 seconds total)