Starting phenix.real_space_refine on Sat Apr 6 17:08:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/04_2024/8t6u_41081_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/04_2024/8t6u_41081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/04_2024/8t6u_41081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/04_2024/8t6u_41081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/04_2024/8t6u_41081_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/04_2024/8t6u_41081_updated.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.003 sd= 0.032 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 2 5.49 5 S 36 5.16 5 C 5826 2.51 5 N 1328 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 681": "OE1" <-> "OE2" Residue "B GLU 777": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8638 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4071 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4071 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" 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 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 Chain: "A" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 256 Unusual residues: {'CLR': 4, 'H9F': 1, 'PC1': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 148 Unusual residues: {'CLR': 4, 'H9F': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Time building chain proxies: 5.47, per 1000 atoms: 0.63 Number of scatterers: 8638 At special positions: 0 Unit cell: (72.092, 132.348, 83.928, 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 36 16.00 P 2 15.00 O 1446 8.00 N 1328 7.00 C 5826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG D 1 " - " ASN A 642 " " NAG L 1 " - " ASN B 642 " Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.6 seconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 2 sheets defined 65.3% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 380 through 392 Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 395 through 400 removed outlier: 5.043A pdb=" N ALA A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 430 removed outlier: 3.709A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 437 through 454 Processing helix chain 'A' and resid 466 through 482 Processing helix chain 'A' and resid 486 through 506 removed outlier: 3.521A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 518 through 546 Processing helix chain 'A' and resid 570 through 592 Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 609 through 623 Processing helix chain 'A' and resid 661 through 689 removed outlier: 5.443A pdb=" N ALA A 668 " --> pdb=" O MET A 664 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Proline residue: A 670 - end of helix Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.650A pdb=" N LEU A 706 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 738 Processing helix chain 'A' and resid 761 through 771 Processing helix chain 'A' and resid 777 through 782 removed outlier: 4.374A pdb=" N ARG A 782 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 800 removed outlier: 3.989A pdb=" N LEU A 800 " --> pdb=" O GLY A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 811 Processing helix chain 'A' and resid 823 through 827 Processing helix chain 'A' and resid 830 through 852 Processing helix chain 'A' and resid 859 through 872 removed outlier: 3.553A pdb=" N LEU A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 866 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) Proline residue: A 868 - end of helix Processing helix chain 'A' and resid 874 through 877 No H-bonds generated for 'chain 'A' and resid 874 through 877' Processing helix chain 'A' and resid 880 through 886 Processing helix chain 'B' and resid 380 through 392 Proline residue: B 391 - end of helix Processing helix chain 'B' and resid 395 through 400 removed outlier: 5.044A pdb=" N ALA B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 430 removed outlier: 3.706A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 437 through 454 Processing helix chain 'B' and resid 466 through 482 Processing helix chain 'B' and resid 486 through 506 removed outlier: 3.520A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 518 through 546 Processing helix chain 'B' and resid 570 through 592 Processing helix chain 'B' and resid 599 through 607 Processing helix chain 'B' and resid 609 through 623 Processing helix chain 'B' and resid 661 through 689 removed outlier: 5.444A pdb=" N ALA B 668 " --> pdb=" O MET B 664 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU B 669 " --> pdb=" O PHE B 665 " (cutoff:3.500A) Proline residue: B 670 - end of helix Processing helix chain 'B' and resid 702 through 719 removed outlier: 3.651A pdb=" N LEU B 706 " --> pdb=" O PHE B 702 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 738 Processing helix chain 'B' and resid 761 through 771 Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.053A pdb=" N ARG B 782 " --> pdb=" O PRO B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 800 removed outlier: 3.989A pdb=" N LEU B 800 " --> pdb=" O GLY B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 811 Processing helix chain 'B' and resid 823 through 827 Processing helix chain 'B' and resid 830 through 852 Processing helix chain 'B' and resid 859 through 872 removed outlier: 3.554A pdb=" N LEU B 865 " --> pdb=" O PHE B 861 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 866 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL B 867 " --> pdb=" O LEU B 863 " (cutoff:3.500A) Proline residue: B 868 - end of helix Processing helix chain 'B' and resid 874 through 877 No H-bonds generated for 'chain 'B' and resid 874 through 877' Processing helix chain 'B' and resid 880 through 886 Processing sheet with id= A, first strand: chain 'A' and resid 739 through 742 removed outlier: 4.056A pdb=" N GLU A 755 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLY A 742 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE A 753 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 739 through 742 removed outlier: 4.056A pdb=" N GLU B 755 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLY B 742 " --> pdb=" O ILE B 753 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE B 753 " --> pdb=" O GLY B 742 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1314 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: 2.37 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1333 1.32 - 1.45: 2348 1.45 - 1.58: 5084 1.58 - 1.71: 5 1.71 - 1.84: 66 Bond restraints: 8836 Sorted by residual: bond pdb=" C5 H9F B2203 " pdb=" N8 H9F B2203 " ideal model delta sigma weight residual 1.348 1.508 -0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" C5 H9F A2204 " pdb=" N8 H9F A2204 " ideal model delta sigma weight residual 1.348 1.487 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C2 H9F B2203 " pdb=" N7 H9F B2203 " ideal model delta sigma weight residual 1.360 1.490 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" C2 H9F A2204 " pdb=" N7 H9F A2204 " ideal model delta sigma weight residual 1.360 1.482 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C6 H9F B2203 " pdb=" N6 H9F B2203 " ideal model delta sigma weight residual 1.364 1.471 -0.107 2.00e-02 2.50e+03 2.86e+01 ... (remaining 8831 not shown) Histogram of bond angle deviations from ideal: 95.40 - 103.26: 100 103.26 - 111.12: 3099 111.12 - 118.98: 4451 118.98 - 126.84: 4315 126.84 - 134.70: 71 Bond angle restraints: 12036 Sorted by residual: angle pdb=" C ILE B 493 " pdb=" N GLY B 494 " pdb=" CA GLY B 494 " ideal model delta sigma weight residual 119.98 125.48 -5.50 1.11e+00 8.12e-01 2.45e+01 angle pdb=" C ILE A 493 " pdb=" N GLY A 494 " pdb=" CA GLY A 494 " ideal model delta sigma weight residual 119.98 125.42 -5.44 1.11e+00 8.12e-01 2.41e+01 angle pdb=" N GLN A 434 " pdb=" CA GLN A 434 " pdb=" C GLN A 434 " ideal model delta sigma weight residual 111.28 106.09 5.19 1.09e+00 8.42e-01 2.27e+01 angle pdb=" N PRO A 722 " pdb=" CA PRO A 722 " pdb=" C PRO A 722 " ideal model delta sigma weight residual 110.55 117.88 -7.33 1.63e+00 3.76e-01 2.02e+01 angle pdb=" N PRO B 722 " pdb=" CA PRO B 722 " pdb=" C PRO B 722 " ideal model delta sigma weight residual 110.55 117.72 -7.17 1.63e+00 3.76e-01 1.94e+01 ... (remaining 12031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 5507 34.06 - 68.12: 167 68.12 - 102.18: 16 102.18 - 136.24: 3 136.24 - 170.30: 1 Dihedral angle restraints: 5694 sinusoidal: 2718 harmonic: 2976 Sorted by residual: dihedral pdb=" C18 H9F A2204 " pdb=" C19 H9F A2204 " pdb=" N7 H9F A2204 " pdb=" C2 H9F A2204 " ideal model delta sinusoidal sigma weight residual 90.87 -98.83 -170.30 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C17 H9F A2204 " pdb=" C18 H9F A2204 " pdb=" C19 H9F A2204 " pdb=" N7 H9F A2204 " ideal model delta sinusoidal sigma weight residual 55.70 -69.79 125.49 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C21 H9F B2203 " pdb=" C22 H9F B2203 " pdb=" C23 H9F B2203 " pdb=" C24 H9F B2203 " ideal model delta sinusoidal sigma weight residual -64.51 52.53 -117.04 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 5691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.848: 1434 0.848 - 1.697: 0 1.697 - 2.545: 0 2.545 - 3.393: 0 3.393 - 4.241: 2 Chirality restraints: 1436 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 1.84 -4.24 2.00e-02 2.50e+03 4.50e+04 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 1.83 -4.23 2.00e-02 2.50e+03 4.48e+04 chirality pdb=" CB ILE A 493 " pdb=" CA ILE A 493 " pdb=" CG1 ILE A 493 " pdb=" CG2 ILE A 493 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1433 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.072 2.00e-02 2.50e+03 6.31e-02 4.98e+01 pdb=" C7 NAG D 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.085 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.068 2.00e-02 2.50e+03 5.99e-02 4.48e+01 pdb=" C7 NAG L 1 " 0.054 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.062 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.081 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 878 " -0.042 2.00e-02 2.50e+03 3.28e-02 1.88e+01 pdb=" CG PHE A 878 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 878 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 878 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 PHE A 878 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 878 " -0.038 2.00e-02 2.50e+03 pdb=" CZ PHE A 878 " -0.020 2.00e-02 2.50e+03 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 905 2.78 - 3.31: 9236 3.31 - 3.84: 14151 3.84 - 4.37: 18683 4.37 - 4.90: 30028 Nonbonded interactions: 73003 Sorted by model distance: nonbonded pdb=" OH TYR A 555 " pdb=" OH TYR B 555 " model vdw 2.246 2.440 nonbonded pdb=" NH2 ARG A 646 " pdb=" CA GLY A 720 " model vdw 2.373 3.520 nonbonded pdb=" NH2 ARG A 879 " pdb=" OE2 GLU A 882 " model vdw 2.403 2.520 nonbonded pdb=" NH2 ARG B 879 " pdb=" OE2 GLU B 882 " model vdw 2.417 2.520 nonbonded pdb=" OG1 THR B 739 " pdb=" O HOH B2301 " model vdw 2.449 2.440 ... (remaining 72998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 369 through 891 or resid 2201 through 2202 or resid 2205)) \ selection = (chain 'B' and (resid 369 through 891 or resid 2201 through 2202 or resid 2205)) \ } ncs_group { reference = chain 'D' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.730 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.150 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 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 : 0.011 0.160 8836 Z= 0.738 Angle : 1.485 7.330 12036 Z= 1.025 Chirality : 0.175 4.241 1436 Planarity : 0.009 0.096 1404 Dihedral : 15.188 170.302 3774 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.64 % Favored : 97.17 % Rotamer: Outliers : 0.33 % Allowed : 5.02 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.20), residues: 1024 helix: -1.70 (0.15), residues: 704 sheet: None (None), residues: 0 loop : -2.66 (0.27), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.009 TRP B 723 HIS 0.018 0.006 HIS B 819 PHE 0.053 0.007 PHE A 878 TYR 0.036 0.009 TYR A 596 ARG 0.014 0.003 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 406 LEU cc_start: 0.9412 (tt) cc_final: 0.9208 (tp) REVERT: A 554 ASN cc_start: 0.8690 (t0) cc_final: 0.8470 (t0) REVERT: B 406 LEU cc_start: 0.9404 (tt) cc_final: 0.9197 (tp) REVERT: B 554 ASN cc_start: 0.8692 (t0) cc_final: 0.8476 (t0) REVERT: B 712 MET cc_start: 0.8731 (mtm) cc_final: 0.8526 (mtm) outliers start: 3 outliers final: 3 residues processed: 135 average time/residue: 0.2371 time to fit residues: 43.2622 Evaluate side-chains 65 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 825 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 26 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8836 Z= 0.195 Angle : 0.572 6.689 12036 Z= 0.279 Chirality : 0.039 0.125 1436 Planarity : 0.005 0.048 1404 Dihedral : 12.250 149.548 1877 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.46 % Allowed : 9.82 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1024 helix: 1.05 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -1.82 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 831 HIS 0.002 0.001 HIS A 819 PHE 0.024 0.001 PHE A 411 TYR 0.010 0.002 TYR B 555 ARG 0.004 0.001 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 69 time to evaluate : 1.117 Fit side-chains REVERT: A 406 LEU cc_start: 0.9302 (tt) cc_final: 0.9086 (tp) REVERT: B 406 LEU cc_start: 0.9301 (tt) cc_final: 0.9085 (tp) outliers start: 22 outliers final: 10 residues processed: 77 average time/residue: 0.1791 time to fit residues: 20.9048 Evaluate side-chains 72 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8836 Z= 0.179 Angle : 0.518 7.890 12036 Z= 0.251 Chirality : 0.038 0.135 1436 Planarity : 0.005 0.052 1404 Dihedral : 11.332 138.980 1875 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.01 % Allowed : 9.82 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1024 helix: 1.76 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.51 (0.30), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 831 HIS 0.002 0.001 HIS A 734 PHE 0.016 0.001 PHE A 411 TYR 0.016 0.001 TYR B 818 ARG 0.005 0.000 ARG B 879 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 65 time to evaluate : 0.931 Fit side-chains REVERT: A 406 LEU cc_start: 0.9368 (tt) cc_final: 0.9151 (tp) REVERT: B 406 LEU cc_start: 0.9363 (tt) cc_final: 0.9150 (tp) outliers start: 27 outliers final: 15 residues processed: 78 average time/residue: 0.1859 time to fit residues: 21.8002 Evaluate side-chains 70 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 889 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8836 Z= 0.201 Angle : 0.516 6.261 12036 Z= 0.247 Chirality : 0.038 0.149 1436 Planarity : 0.005 0.053 1404 Dihedral : 10.563 130.345 1874 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.57 % Allowed : 9.49 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1024 helix: 1.86 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.27 (0.30), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 831 HIS 0.001 0.000 HIS B 819 PHE 0.012 0.001 PHE B 411 TYR 0.016 0.001 TYR A 824 ARG 0.004 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 56 time to evaluate : 0.957 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 68 average time/residue: 0.1876 time to fit residues: 19.1637 Evaluate side-chains 69 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 889 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 683 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8836 Z= 0.319 Angle : 0.574 7.015 12036 Z= 0.274 Chirality : 0.040 0.151 1436 Planarity : 0.005 0.054 1404 Dihedral : 10.130 114.229 1874 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.34 % Allowed : 9.93 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1024 helix: 1.80 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.04 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 831 HIS 0.002 0.001 HIS A 734 PHE 0.011 0.001 PHE A 471 TYR 0.012 0.002 TYR A 824 ARG 0.005 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 53 time to evaluate : 0.968 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 63 average time/residue: 0.1922 time to fit residues: 18.1988 Evaluate side-chains 68 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 877 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8836 Z= 0.197 Angle : 0.514 5.722 12036 Z= 0.246 Chirality : 0.038 0.142 1436 Planarity : 0.004 0.055 1404 Dihedral : 9.458 87.852 1874 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.46 % Allowed : 9.93 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.27), residues: 1024 helix: 1.92 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.92 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 831 HIS 0.001 0.000 HIS B 703 PHE 0.013 0.001 PHE B 411 TYR 0.012 0.001 TYR A 824 ARG 0.004 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 1.055 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 70 average time/residue: 0.1842 time to fit residues: 19.5906 Evaluate side-chains 68 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8836 Z= 0.283 Angle : 0.562 7.091 12036 Z= 0.267 Chirality : 0.039 0.150 1436 Planarity : 0.005 0.054 1404 Dihedral : 9.242 86.978 1874 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.57 % Allowed : 10.27 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.27), residues: 1024 helix: 1.90 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.77 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 831 HIS 0.001 0.001 HIS B 703 PHE 0.010 0.001 PHE A 411 TYR 0.011 0.001 TYR A 824 ARG 0.004 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 54 time to evaluate : 0.985 Fit side-chains outliers start: 23 outliers final: 18 residues processed: 67 average time/residue: 0.1862 time to fit residues: 18.7469 Evaluate side-chains 70 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 52 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 877 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.0980 chunk 62 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.0770 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8836 Z= 0.145 Angle : 0.527 7.214 12036 Z= 0.250 Chirality : 0.038 0.177 1436 Planarity : 0.005 0.054 1404 Dihedral : 8.919 87.751 1874 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.90 % Allowed : 11.05 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.27), residues: 1024 helix: 1.98 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -0.55 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 492 HIS 0.001 0.000 HIS B 819 PHE 0.014 0.001 PHE A 411 TYR 0.013 0.001 TYR A 824 ARG 0.011 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 406 LEU cc_start: 0.9421 (tt) cc_final: 0.9209 (tp) REVERT: B 406 LEU cc_start: 0.9436 (tt) cc_final: 0.9230 (tp) outliers start: 17 outliers final: 11 residues processed: 76 average time/residue: 0.1798 time to fit residues: 20.6448 Evaluate side-chains 68 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 889 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 91 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 96 optimal weight: 0.0170 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8836 Z= 0.163 Angle : 0.533 8.424 12036 Z= 0.249 Chirality : 0.039 0.303 1436 Planarity : 0.005 0.054 1404 Dihedral : 8.604 86.760 1874 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.45 % Allowed : 11.50 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.27), residues: 1024 helix: 2.07 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.58 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 492 HIS 0.001 0.000 HIS B 819 PHE 0.011 0.001 PHE A 411 TYR 0.013 0.001 TYR A 824 ARG 0.011 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.907 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.1921 time to fit residues: 19.8648 Evaluate side-chains 68 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8836 Z= 0.180 Angle : 0.545 8.584 12036 Z= 0.255 Chirality : 0.038 0.160 1436 Planarity : 0.005 0.054 1404 Dihedral : 8.425 86.859 1874 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.34 % Allowed : 11.50 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.27), residues: 1024 helix: 2.05 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.45 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 492 HIS 0.001 0.000 HIS B 819 PHE 0.012 0.001 PHE A 411 TYR 0.013 0.001 TYR A 824 ARG 0.010 0.000 ARG A 603 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.912 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 72 average time/residue: 0.1791 time to fit residues: 19.4872 Evaluate side-chains 74 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.071767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.060956 restraints weight = 25201.144| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.96 r_work: 0.2850 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8836 Z= 0.186 Angle : 0.547 8.841 12036 Z= 0.253 Chirality : 0.038 0.145 1436 Planarity : 0.005 0.054 1404 Dihedral : 8.306 86.777 1874 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.45 % Allowed : 12.17 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.27), residues: 1024 helix: 2.04 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 831 HIS 0.001 0.000 HIS B 819 PHE 0.011 0.001 PHE A 411 TYR 0.013 0.001 TYR A 824 ARG 0.008 0.000 ARG A 603 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1774.14 seconds wall clock time: 33 minutes 10.65 seconds (1990.65 seconds total)