Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 05:49:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/10_2023/8t6u_41081_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/10_2023/8t6u_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_41081/10_2023/8t6u_41081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/10_2023/8t6u_41081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/10_2023/8t6u_41081_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/10_2023/8t6u_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-1.21rc1-5097/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 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 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: 5.10, per 1000 atoms: 0.59 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: 3.48 Conformation dependent library (CDL) restraints added in 1.4 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: 1.56 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: 2.81 Time building geometry restraints manager: 3.77 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: 4971 34.06 - 68.12: 153 68.12 - 102.18: 16 102.18 - 136.24: 3 136.24 - 170.30: 1 Dihedral angle restraints: 5144 sinusoidal: 2168 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 5141 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: 2.460 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: 7.920 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.330 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.430 ------------------------------------------------------------------------------- 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 : 15.930 170.302 3224 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 *********************** 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 : 0.967 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 135 average time/residue: 0.2318 time to fit residues: 42.1060 Evaluate side-chains 66 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0765 time to fit residues: 1.6211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 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: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8836 Z= 0.201 Angle : 0.585 6.667 12036 Z= 0.284 Chirality : 0.038 0.130 1436 Planarity : 0.005 0.047 1404 Dihedral : 13.421 150.074 1324 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.34 % Allowed : 9.49 % Favored : 88.17 % 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: 0.17 (0.25), residues: 1024 helix: 1.04 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -1.99 (0.28), residues: 322 *********************** 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 90 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 0.954 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 76 average time/residue: 0.1797 time to fit residues: 20.5097 Evaluate side-chains 68 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0875 time to fit residues: 2.5491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 77 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8675 moved from start: 0.2201 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= 0.169 Angle : 0.529 7.881 12036 Z= 0.254 Chirality : 0.038 0.140 1436 Planarity : 0.005 0.052 1404 Dihedral : 12.488 139.456 1324 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.01 % Allowed : 9.26 % Favored : 88.73 % 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: 1.15 (0.26), residues: 1024 helix: 1.75 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.56 (0.30), residues: 320 *********************** 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 82 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 1.024 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 73 average time/residue: 0.1842 time to fit residues: 20.3077 Evaluate side-chains 63 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0866 time to fit residues: 2.8856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0570 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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: 0.8674 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8836 Z= 0.157 Angle : 0.506 6.795 12036 Z= 0.240 Chirality : 0.037 0.147 1436 Planarity : 0.005 0.053 1404 Dihedral : 11.693 132.046 1324 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.89 % Allowed : 9.71 % Favored : 89.40 % 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: 1.44 (0.26), residues: 1024 helix: 1.91 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.36 (0.31), residues: 312 *********************** 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 72 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.864 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 68 average time/residue: 0.1901 time to fit residues: 19.3954 Evaluate side-chains 56 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0845 time to fit residues: 1.4574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 40 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 0.0270 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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: 0.8686 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8836 Z= 0.173 Angle : 0.501 6.073 12036 Z= 0.238 Chirality : 0.037 0.141 1436 Planarity : 0.005 0.053 1404 Dihedral : 11.269 124.046 1324 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.89 % Allowed : 10.38 % Favored : 88.73 % 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: 2.00 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.03 (0.32), residues: 320 *********************** 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 67 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.899 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.1945 time to fit residues: 18.0126 Evaluate side-chains 62 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0846 time to fit residues: 2.0461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 95 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.8696 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8836 Z= 0.180 Angle : 0.514 7.290 12036 Z= 0.242 Chirality : 0.037 0.142 1436 Planarity : 0.004 0.053 1404 Dihedral : 10.707 109.121 1324 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.89 % Allowed : 10.83 % Favored : 88.28 % 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: 1.69 (0.27), residues: 1024 helix: 1.98 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -0.92 (0.32), residues: 314 *********************** 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 73 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 1.043 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 70 average time/residue: 0.1840 time to fit residues: 19.5620 Evaluate side-chains 61 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0829 time to fit residues: 1.4988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.8711 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8836 Z= 0.206 Angle : 0.530 6.293 12036 Z= 0.248 Chirality : 0.038 0.147 1436 Planarity : 0.004 0.053 1404 Dihedral : 9.912 83.713 1324 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.78 % Allowed : 11.27 % 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: 1.74 (0.27), residues: 1024 helix: 2.01 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -0.86 (0.33), residues: 314 *********************** 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 71 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.921 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 68 average time/residue: 0.1934 time to fit residues: 19.7656 Evaluate side-chains 63 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0857 time to fit residues: 1.7807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8705 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8836 Z= 0.186 Angle : 0.537 7.228 12036 Z= 0.251 Chirality : 0.038 0.211 1436 Planarity : 0.004 0.053 1404 Dihedral : 9.703 83.736 1324 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.56 % Allowed : 12.39 % 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: 1.81 (0.27), residues: 1024 helix: 2.02 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -0.73 (0.33), residues: 314 *********************** 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 70 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.857 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.1864 time to fit residues: 18.8799 Evaluate side-chains 62 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0988 time to fit residues: 1.9280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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: 0.8703 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8836 Z= 0.177 Angle : 0.546 8.890 12036 Z= 0.252 Chirality : 0.039 0.307 1436 Planarity : 0.005 0.053 1404 Dihedral : 9.503 83.999 1324 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.45 % Allowed : 12.50 % 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: 1.91 (0.27), residues: 1024 helix: 2.06 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.55 (0.34), residues: 318 *********************** 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 65 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.915 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 65 average time/residue: 0.1945 time to fit residues: 18.8793 Evaluate side-chains 61 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0765 time to fit residues: 1.5132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 62 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.0870 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 11 optimal weight: 0.0030 overall best weight: 0.1166 ------------------------------------------------------------------------------- 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: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 8836 Z= 0.145 Angle : 0.536 9.547 12036 Z= 0.247 Chirality : 0.038 0.199 1436 Planarity : 0.004 0.053 1404 Dihedral : 9.259 83.241 1324 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 12.95 % 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: 1.95 (0.27), residues: 1024 helix: 2.07 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -0.50 (0.35), residues: 314 ********************** 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 73 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.980 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1874 time to fit residues: 20.6836 Evaluate side-chains 63 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.3980 chunk 81 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.072623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061612 restraints weight = 25202.202| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.97 r_work: 0.2854 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8836 Z= 0.232 Angle : 0.583 9.368 12036 Z= 0.270 Chirality : 0.040 0.301 1436 Planarity : 0.004 0.053 1404 Dihedral : 9.176 85.079 1324 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.11 % Allowed : 13.28 % Favored : 86.61 % 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: 1.94 (0.27), residues: 1024 helix: 2.03 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -0.41 (0.35), residues: 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1761.09 seconds wall clock time: 32 minutes 49.16 seconds (1969.16 seconds total)