Starting phenix.real_space_refine on Wed Feb 14 04:33:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tya_26171/02_2024/7tya_26171_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tya_26171/02_2024/7tya_26171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tya_26171/02_2024/7tya_26171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tya_26171/02_2024/7tya_26171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tya_26171/02_2024/7tya_26171_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tya_26171/02_2024/7tya_26171_updated.pdb" } resolution = 3.07 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= -0.002 sd= 0.033 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 5794 2.51 5 N 1312 2.21 5 O 1473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 485": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 535": "OE1" <-> "OE2" Residue "B TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8617 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4085 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'KR3:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4085 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'KR3:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" 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: "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: "A" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 166 Unusual residues: {'CLR': 4, 'PC1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 166 Unusual residues: {'CLR': 4, 'PC1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Time building chain proxies: 5.14, per 1000 atoms: 0.60 Number of scatterers: 8617 At special positions: 0 Unit cell: (133.209, 72.561, 84.474, 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 1473 8.00 N 1312 7.00 C 5794 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 642 " " NAG D 1 " - " ASN B 642 " Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.6 seconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 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 0 sheets defined 64.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 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: 5.280A pdb=" N ALA A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 430 removed outlier: 3.720A 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: 3.732A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 515 Processing helix chain 'A' and resid 518 through 546 removed outlier: 3.535A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 543 " --> pdb=" O KR3 A 539 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 593 removed outlier: 3.642A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) 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: 3.612A pdb=" N PHE A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ALA A 668 " --> pdb=" O MET A 664 " (cutoff:3.500A) removed outlier: 5.083A 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: 3.647A pdb=" N LEU A 706 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 3.957A 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 772 Processing helix chain 'A' and resid 777 through 782 removed outlier: 4.291A pdb=" N ARG A 782 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 798 Processing helix chain 'A' and resid 804 through 811 Processing helix chain 'A' and resid 823 through 826 No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 830 through 852 Processing helix chain 'A' and resid 860 through 872 removed outlier: 3.808A pdb=" N THR A 866 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 4.362A 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: 5.279A pdb=" N ALA B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 430 removed outlier: 3.718A 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: 3.734A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 515 Processing helix chain 'B' and resid 518 through 546 removed outlier: 3.536A pdb=" N LEU B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 593 removed outlier: 3.643A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) 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: 3.607A pdb=" N PHE B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ALA B 668 " --> pdb=" O MET B 664 " (cutoff:3.500A) removed outlier: 5.085A 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: 3.647A pdb=" N LEU B 706 " --> pdb=" O PHE B 702 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 3.956A 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 774 removed outlier: 4.998A pdb=" N ILE B 774 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.290A pdb=" N ARG B 782 " --> pdb=" O PRO B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 798 Processing helix chain 'B' and resid 804 through 811 Processing helix chain 'B' and resid 823 through 826 No H-bonds generated for 'chain 'B' and resid 823 through 826' Processing helix chain 'B' and resid 830 through 852 Processing helix chain 'B' and resid 860 through 872 removed outlier: 3.807A pdb=" N THR B 866 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 4.362A 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 886 436 hydrogen bonds defined for protein. 1284 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: 2.24 Time building geometry restraints manager: 4.06 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: 1248 1.32 - 1.45: 2278 1.45 - 1.57: 5186 1.57 - 1.69: 8 1.69 - 1.82: 66 Bond restraints: 8786 Sorted by residual: bond pdb=" NZ KR3 A 539 " pdb=" C1 KR3 A 539 " ideal model delta sigma weight residual 1.344 1.677 -0.333 2.00e-02 2.50e+03 2.77e+02 bond pdb=" NZ KR3 B 539 " pdb=" C1 KR3 B 539 " ideal model delta sigma weight residual 1.344 1.676 -0.332 2.00e-02 2.50e+03 2.76e+02 bond pdb=" NZ KR3 B 851 " pdb=" C1 KR3 B 851 " ideal model delta sigma weight residual 1.344 1.665 -0.321 2.00e-02 2.50e+03 2.57e+02 bond pdb=" NZ KR3 A 851 " pdb=" C1 KR3 A 851 " ideal model delta sigma weight residual 1.344 1.664 -0.320 2.00e-02 2.50e+03 2.56e+02 bond pdb=" N ILE B 783 " pdb=" CA ILE B 783 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.50e-03 1.78e+04 2.33e+01 ... (remaining 8781 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.48: 298 105.48 - 112.68: 4487 112.68 - 119.87: 3879 119.87 - 127.07: 3247 127.07 - 134.27: 55 Bond angle restraints: 11966 Sorted by residual: angle pdb=" N PRO A 816 " pdb=" CA PRO A 816 " pdb=" C PRO A 816 " ideal model delta sigma weight residual 113.86 102.18 11.68 1.25e+00 6.40e-01 8.73e+01 angle pdb=" N CYS A 885 " pdb=" CA CYS A 885 " pdb=" C CYS A 885 " ideal model delta sigma weight residual 111.11 117.71 -6.60 1.20e+00 6.94e-01 3.02e+01 angle pdb=" N CYS B 885 " pdb=" CA CYS B 885 " pdb=" C CYS B 885 " ideal model delta sigma weight residual 111.11 117.68 -6.57 1.20e+00 6.94e-01 3.00e+01 angle pdb=" N THR B 853 " pdb=" CA THR B 853 " pdb=" C THR B 853 " ideal model delta sigma weight residual 110.08 102.76 7.32 1.38e+00 5.25e-01 2.82e+01 angle pdb=" CA GLY B 699 " pdb=" C GLY B 699 " pdb=" O GLY B 699 " ideal model delta sigma weight residual 122.45 118.65 3.80 7.20e-01 1.93e+00 2.79e+01 ... (remaining 11961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 5370 25.61 - 51.21: 220 51.21 - 76.82: 46 76.82 - 102.42: 8 102.42 - 128.02: 4 Dihedral angle restraints: 5648 sinusoidal: 2672 harmonic: 2976 Sorted by residual: dihedral pdb=" CG KR3 A 851 " pdb=" CD KR3 A 851 " pdb=" CE KR3 A 851 " pdb=" NZ KR3 A 851 " ideal model delta sinusoidal sigma weight residual 176.95 48.93 128.02 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" CG KR3 B 851 " pdb=" CD KR3 B 851 " pdb=" CE KR3 B 851 " pdb=" NZ KR3 B 851 " ideal model delta sinusoidal sigma weight residual 176.95 49.14 127.81 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C1 CLR A2204 " pdb=" C2 CLR A2204 " pdb=" C3 CLR A2204 " pdb=" C4 CLR A2204 " ideal model delta sinusoidal sigma weight residual 57.41 -62.56 119.97 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 5645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 685 0.066 - 0.132: 584 0.132 - 0.199: 161 0.199 - 0.265: 4 0.265 - 0.331: 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 -2.21 -0.19 2.00e-02 2.50e+03 9.50e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.38e+01 chirality pdb=" CA LEU A 883 " pdb=" N LEU A 883 " pdb=" C LEU A 883 " pdb=" CB LEU A 883 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 1433 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.303 2.00e-02 2.50e+03 2.55e-01 8.12e+02 pdb=" C7 NAG C 1 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.436 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.300 2.00e-02 2.50e+03 2.52e-01 7.95e+02 pdb=" C7 NAG D 1 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.190 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.430 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.235 2.00e-02 2.50e+03 1.95e-01 4.75e+02 pdb=" C7 NAG C 2 " 0.062 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.322 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.014 2.00e-02 2.50e+03 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 276 2.74 - 3.28: 8843 3.28 - 3.82: 13093 3.82 - 4.36: 17989 4.36 - 4.90: 29702 Nonbonded interactions: 69903 Sorted by model distance: nonbonded pdb=" OG1 THR B 798 " pdb=" O HOH B2301 " model vdw 2.203 2.440 nonbonded pdb=" OG1 THR A 798 " pdb=" O HOH A2301 " model vdw 2.208 2.440 nonbonded pdb=" OG SER A 465 " pdb=" O HOH A2302 " model vdw 2.305 2.440 nonbonded pdb=" OG SER B 465 " pdb=" O HOH B2302 " model vdw 2.389 2.440 nonbonded pdb=" NH2 ARG A 808 " pdb=" OE1 GLN A 840 " model vdw 2.411 2.520 ... (remaining 69898 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.820 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: 8.110 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.770 Find NCS groups from input model: 0.430 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 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 : 0.015 0.333 8786 Z= 0.933 Angle : 1.807 15.351 11966 Z= 1.358 Chirality : 0.086 0.331 1436 Planarity : 0.012 0.255 1404 Dihedral : 14.940 128.024 3728 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.22 % Allowed : 3.24 % Favored : 96.53 % 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: -2.11 (0.23), residues: 1012 helix: -1.07 (0.17), residues: 668 sheet: None (None), residues: 0 loop : -1.79 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 492 HIS 0.005 0.001 HIS A 834 PHE 0.016 0.002 PHE A 464 TYR 0.012 0.003 TYR B 393 ARG 0.005 0.001 ARG A 730 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8744 (mt-10) REVERT: A 663 MET cc_start: 0.8610 (tpp) cc_final: 0.8370 (tpt) REVERT: A 741 MET cc_start: 0.9330 (mmm) cc_final: 0.9045 (mmm) REVERT: B 429 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8709 (mt-10) REVERT: B 741 MET cc_start: 0.9321 (mmm) cc_final: 0.8958 (mmm) outliers start: 2 outliers final: 0 residues processed: 74 average time/residue: 0.2241 time to fit residues: 23.3979 Evaluate side-chains 42 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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: 0.8980 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 593 ASN B 550 GLN B 593 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8786 Z= 0.224 Angle : 0.593 8.632 11966 Z= 0.289 Chirality : 0.039 0.133 1436 Planarity : 0.004 0.042 1404 Dihedral : 10.185 89.613 1838 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.11 % Allowed : 5.70 % Favored : 94.18 % 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: 1.00 (0.26), residues: 1012 helix: 1.53 (0.19), residues: 674 sheet: None (None), residues: 0 loop : -1.12 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 831 HIS 0.003 0.001 HIS A 734 PHE 0.015 0.001 PHE A 411 TYR 0.013 0.002 TYR A 824 ARG 0.004 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.992 Fit side-chains REVERT: A 741 MET cc_start: 0.9323 (mmm) cc_final: 0.8792 (mmm) REVERT: A 776 MET cc_start: 0.9332 (ptp) cc_final: 0.9120 (ptp) REVERT: B 741 MET cc_start: 0.9346 (mmm) cc_final: 0.8838 (mmm) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.1597 time to fit residues: 12.2324 Evaluate side-chains 41 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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: 6.9990 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 ASN ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8786 Z= 0.233 Angle : 0.536 10.690 11966 Z= 0.262 Chirality : 0.039 0.132 1436 Planarity : 0.004 0.048 1404 Dihedral : 9.158 83.406 1838 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.78 % Allowed : 6.15 % Favored : 93.06 % 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: 1.63 (0.27), residues: 1012 helix: 2.05 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -1.07 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 662 HIS 0.002 0.000 HIS B 734 PHE 0.012 0.001 PHE A 411 TYR 0.011 0.001 TYR A 824 ARG 0.002 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.996 Fit side-chains REVERT: A 741 MET cc_start: 0.9305 (mmm) cc_final: 0.8533 (mmm) REVERT: A 853 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8926 (t) REVERT: B 741 MET cc_start: 0.9324 (mmm) cc_final: 0.8583 (mmm) outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 0.2135 time to fit residues: 15.5599 Evaluate side-chains 49 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 872 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 0.0470 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8786 Z= 0.252 Angle : 0.527 8.377 11966 Z= 0.254 Chirality : 0.038 0.124 1436 Planarity : 0.004 0.049 1404 Dihedral : 8.910 78.113 1838 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.78 % Allowed : 6.94 % Favored : 92.28 % 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: 2.00 (0.27), residues: 1012 helix: 2.27 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.79 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 662 HIS 0.001 0.000 HIS B 734 PHE 0.010 0.001 PHE A 411 TYR 0.011 0.001 TYR B 486 ARG 0.003 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 1.013 Fit side-chains REVERT: A 664 MET cc_start: 0.9128 (mtm) cc_final: 0.8825 (mtm) REVERT: A 741 MET cc_start: 0.9252 (mmm) cc_final: 0.8751 (mmm) REVERT: B 664 MET cc_start: 0.9201 (mtm) cc_final: 0.8889 (mtm) REVERT: B 741 MET cc_start: 0.9271 (mmm) cc_final: 0.8736 (mmm) REVERT: B 853 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8905 (t) outliers start: 7 outliers final: 2 residues processed: 49 average time/residue: 0.2087 time to fit residues: 15.2907 Evaluate side-chains 47 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 872 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.0030 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 88 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.3930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8786 Z= 0.141 Angle : 0.489 9.678 11966 Z= 0.236 Chirality : 0.037 0.120 1436 Planarity : 0.004 0.050 1404 Dihedral : 8.507 71.543 1838 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.12 % Allowed : 7.49 % Favored : 91.39 % 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: 2.26 (0.27), residues: 1012 helix: 2.48 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.68 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 662 HIS 0.002 0.000 HIS A 734 PHE 0.010 0.001 PHE A 471 TYR 0.010 0.001 TYR A 486 ARG 0.004 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.943 Fit side-chains REVERT: A 741 MET cc_start: 0.9228 (mmm) cc_final: 0.8687 (mmm) REVERT: A 853 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8886 (t) REVERT: B 741 MET cc_start: 0.9237 (mmm) cc_final: 0.8703 (mmm) REVERT: B 853 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8872 (t) outliers start: 10 outliers final: 2 residues processed: 57 average time/residue: 0.2024 time to fit residues: 17.1779 Evaluate side-chains 50 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 853 THR 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: 3.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN A 759 GLN B 433 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8786 Z= 0.361 Angle : 0.583 10.461 11966 Z= 0.278 Chirality : 0.040 0.202 1436 Planarity : 0.004 0.050 1404 Dihedral : 8.713 67.789 1838 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.57 % Allowed : 7.72 % Favored : 90.72 % 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: 2.19 (0.28), residues: 1012 helix: 2.31 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -0.46 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 662 HIS 0.002 0.000 HIS A 819 PHE 0.011 0.001 PHE A 526 TYR 0.010 0.001 TYR A 486 ARG 0.003 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 1.041 Fit side-chains REVERT: A 663 MET cc_start: 0.9179 (tpp) cc_final: 0.8871 (tpp) REVERT: A 664 MET cc_start: 0.9289 (mtm) cc_final: 0.8840 (mtm) REVERT: A 741 MET cc_start: 0.9188 (mmm) cc_final: 0.8717 (mmm) REVERT: A 853 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8943 (t) REVERT: B 663 MET cc_start: 0.9212 (tpp) cc_final: 0.8970 (tpp) REVERT: B 664 MET cc_start: 0.9108 (mtm) cc_final: 0.8861 (mtm) REVERT: B 741 MET cc_start: 0.9198 (mmm) cc_final: 0.8759 (mmm) REVERT: B 853 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8934 (t) outliers start: 14 outliers final: 4 residues processed: 54 average time/residue: 0.2269 time to fit residues: 17.6143 Evaluate side-chains 47 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 872 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 0.0000 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN B 593 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8786 Z= 0.149 Angle : 0.494 8.771 11966 Z= 0.239 Chirality : 0.037 0.135 1436 Planarity : 0.004 0.051 1404 Dihedral : 8.342 64.303 1838 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.78 % Allowed : 7.94 % Favored : 91.28 % 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: 2.44 (0.27), residues: 1012 helix: 2.66 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -0.50 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 492 HIS 0.002 0.000 HIS A 734 PHE 0.010 0.001 PHE A 471 TYR 0.011 0.001 TYR B 519 ARG 0.002 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.894 Fit side-chains REVERT: A 664 MET cc_start: 0.9245 (mtm) cc_final: 0.8899 (mtm) REVERT: A 741 MET cc_start: 0.9202 (mmm) cc_final: 0.8746 (mmm) REVERT: A 795 MET cc_start: 0.8826 (mtp) cc_final: 0.8575 (mtm) REVERT: A 853 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8903 (t) REVERT: B 663 MET cc_start: 0.9132 (tpp) cc_final: 0.8923 (tpp) REVERT: B 741 MET cc_start: 0.9212 (mmm) cc_final: 0.8618 (mmm) REVERT: B 853 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8896 (t) outliers start: 7 outliers final: 5 residues processed: 58 average time/residue: 0.1944 time to fit residues: 16.6678 Evaluate side-chains 51 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 872 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 91 optimal weight: 0.0050 chunk 55 optimal weight: 0.9980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN B 593 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8786 Z= 0.151 Angle : 0.495 11.399 11966 Z= 0.239 Chirality : 0.037 0.133 1436 Planarity : 0.004 0.051 1404 Dihedral : 8.190 61.246 1838 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.01 % Allowed : 8.17 % Favored : 90.83 % 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: 2.49 (0.27), residues: 1012 helix: 2.68 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -0.49 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 662 HIS 0.002 0.000 HIS B 734 PHE 0.011 0.001 PHE B 526 TYR 0.009 0.001 TYR B 519 ARG 0.002 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.992 Fit side-chains REVERT: A 664 MET cc_start: 0.9226 (mtm) cc_final: 0.8904 (mtm) REVERT: A 741 MET cc_start: 0.9212 (mmm) cc_final: 0.8620 (mmm) REVERT: A 853 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8873 (t) REVERT: B 663 MET cc_start: 0.9111 (tpp) cc_final: 0.8832 (tpp) REVERT: B 741 MET cc_start: 0.9221 (mmm) cc_final: 0.8630 (mmm) REVERT: B 853 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8879 (t) outliers start: 9 outliers final: 5 residues processed: 56 average time/residue: 0.1978 time to fit residues: 16.4925 Evaluate side-chains 50 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 872 VAL 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: 0.7980 chunk 28 optimal weight: 0.0000 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN B 593 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8786 Z= 0.160 Angle : 0.489 9.811 11966 Z= 0.236 Chirality : 0.037 0.131 1436 Planarity : 0.004 0.051 1404 Dihedral : 8.075 58.750 1838 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.78 % Allowed : 8.50 % Favored : 90.72 % 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: 2.55 (0.27), residues: 1012 helix: 2.71 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.38 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 662 HIS 0.002 0.000 HIS A 734 PHE 0.009 0.001 PHE A 471 TYR 0.010 0.001 TYR B 519 ARG 0.003 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 664 MET cc_start: 0.9214 (mtm) cc_final: 0.8780 (mtm) REVERT: A 741 MET cc_start: 0.9197 (mmm) cc_final: 0.8602 (mmm) REVERT: A 853 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8865 (t) REVERT: B 663 MET cc_start: 0.9046 (tpp) cc_final: 0.8752 (tpt) REVERT: B 853 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8866 (t) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 0.2007 time to fit residues: 16.3697 Evaluate side-chains 51 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 872 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN B 593 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8786 Z= 0.141 Angle : 0.482 10.066 11966 Z= 0.234 Chirality : 0.037 0.169 1436 Planarity : 0.004 0.049 1404 Dihedral : 7.954 59.328 1838 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.67 % Allowed : 8.72 % Favored : 90.60 % 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: 2.61 (0.27), residues: 1012 helix: 2.76 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -0.38 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 662 HIS 0.002 0.000 HIS B 734 PHE 0.009 0.001 PHE A 471 TYR 0.010 0.001 TYR B 519 ARG 0.003 0.000 ARG A 603 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 741 MET cc_start: 0.9199 (mmm) cc_final: 0.8574 (mmm) REVERT: A 853 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8890 (t) REVERT: B 663 MET cc_start: 0.9034 (tpp) cc_final: 0.8456 (tpp) REVERT: B 741 MET cc_start: 0.9209 (mmm) cc_final: 0.8585 (mmm) REVERT: B 853 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8881 (t) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.2009 time to fit residues: 16.0639 Evaluate side-chains 50 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 872 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN B 593 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.055261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.045129 restraints weight = 26408.722| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 3.06 r_work: 0.2385 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8786 Z= 0.170 Angle : 0.489 9.673 11966 Z= 0.238 Chirality : 0.037 0.201 1436 Planarity : 0.004 0.048 1404 Dihedral : 7.916 59.231 1838 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.56 % Allowed : 9.06 % Favored : 90.38 % 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: 2.57 (0.27), residues: 1012 helix: 2.75 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -0.44 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 662 HIS 0.002 0.000 HIS B 734 PHE 0.009 0.001 PHE A 471 TYR 0.010 0.001 TYR B 519 ARG 0.002 0.000 ARG A 603 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1714.47 seconds wall clock time: 32 minutes 5.98 seconds (1925.98 seconds total)