Starting phenix.real_space_refine on Tue Mar 3 23:16:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tya_26171/03_2026/7tya_26171.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tya_26171/03_2026/7tya_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tya_26171/03_2026/7tya_26171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tya_26171/03_2026/7tya_26171.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tya_26171/03_2026/7tya_26171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tya_26171/03_2026/7tya_26171.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8617 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1351 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KR3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2397 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KR3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 309 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 4, 'TRANS': 35} Chain: "B" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1351 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KR3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2397 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KR3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 309 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 4, 'TRANS': 35} 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: 1.92, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, 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 " Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 306.9 milliseconds 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... Secondary structure from input PDB file: 52 helices and 4 sheets defined 71.9% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.710A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) 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 436 through 455 Processing helix chain 'A' and resid 465 through 483 Processing helix chain 'A' and resid 485 through 507 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 508 through 516 removed outlier: 3.873A pdb=" N PHE A 511 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 547 Processing helix chain 'A' and resid 569 through 594 removed outlier: 3.642A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.611A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 667 Processing helix chain 'A' and resid 667 through 690 Processing helix chain 'A' and resid 701 through 717 removed outlier: 3.767A pdb=" N ASP A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 706 " --> pdb=" O PHE A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 727 through 738 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 776 through 781 removed outlier: 3.664A pdb=" N LEU A 780 " --> pdb=" O MET A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 799 removed outlier: 3.774A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 859 through 865 Processing helix chain 'A' and resid 865 through 873 Processing helix chain 'A' and resid 879 through 887 Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.710A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) 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 436 through 455 Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 485 through 507 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 508 through 516 removed outlier: 3.874A pdb=" N PHE B 511 " --> pdb=" O GLU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 547 Processing helix chain 'B' and resid 569 through 594 removed outlier: 3.643A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.612A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 667 Processing helix chain 'B' and resid 667 through 690 Processing helix chain 'B' and resid 701 through 717 removed outlier: 3.766A pdb=" N ASP B 705 " --> pdb=" O GLY B 701 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 706 " --> pdb=" O PHE B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 720 No H-bonds generated for 'chain 'B' and resid 718 through 720' Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 760 through 773 Processing helix chain 'B' and resid 776 through 781 removed outlier: 3.664A pdb=" N LEU B 780 " --> pdb=" O MET B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 799 removed outlier: 3.776A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 812 Processing helix chain 'B' and resid 822 through 827 Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 859 through 865 Processing helix chain 'B' and resid 865 through 873 Processing helix chain 'B' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 742 removed outlier: 7.128A pdb=" N VAL A 740 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A 752 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 742 removed outlier: 7.126A pdb=" N VAL B 740 " --> pdb=" O GLN B 754 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 752 " --> pdb=" O GLY B 742 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.07 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: 2270 1.45 - 1.57: 5186 1.57 - 1.69: 8 1.69 - 1.82: 66 Bond restraints: 8778 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 8773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 10799 3.07 - 6.14: 1128 6.14 - 9.21: 10 9.21 - 12.28: 3 12.28 - 15.35: 2 Bond angle restraints: 11942 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 11937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 5362 25.61 - 51.21: 220 51.21 - 76.82: 46 76.82 - 102.42: 8 102.42 - 128.02: 4 Dihedral angle restraints: 5640 sinusoidal: 2672 harmonic: 2968 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 5637 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: 1398 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 1395 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 274 2.74 - 3.28: 8798 3.28 - 3.82: 13031 3.82 - 4.36: 17878 4.36 - 4.90: 29682 Nonbonded interactions: 69663 Sorted by model distance: nonbonded pdb=" OG1 THR B 798 " pdb=" O HOH B2301 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR A 798 " pdb=" O HOH A2301 " model vdw 2.208 3.040 nonbonded pdb=" OG SER A 465 " pdb=" O HOH A2302 " model vdw 2.305 3.040 nonbonded pdb=" OG SER B 465 " pdb=" O HOH B2302 " model vdw 2.389 3.040 nonbonded pdb=" NH2 ARG A 808 " pdb=" OE1 GLN A 840 " model vdw 2.411 3.120 ... (remaining 69658 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 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: 2.580 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.900 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.960 ------------------------------------------------------------------------------- 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 8790 Z= 1.107 Angle : 1.815 15.351 11954 Z= 1.360 Chirality : 0.086 0.331 1436 Planarity : 0.013 0.255 1396 Dihedral : 14.955 128.024 3720 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.23), residues: 1012 helix: -1.07 (0.17), residues: 666 sheet: None (None), residues: 0 loop : -1.71 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 730 TYR 0.012 0.003 TYR B 393 PHE 0.016 0.002 PHE A 464 TRP 0.024 0.003 TRP A 492 HIS 0.005 0.001 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.01493 ( 8778) covalent geometry : angle 1.80783 (11942) hydrogen bonds : bond 0.24649 ( 496) hydrogen bonds : angle 8.33089 ( 1452) Misc. bond : bond 0.10089 ( 8) link_BETA1-4 : bond 0.00578 ( 2) link_BETA1-4 : angle 1.07894 ( 6) link_NAG-ASN : bond 0.00299 ( 2) link_NAG-ASN : angle 7.32054 ( 6) *********************** 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 to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.310 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: 0.0989 time to fit residues: 10.2425 Evaluate side-chains 42 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.055275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.044875 restraints weight = 26498.000| |-----------------------------------------------------------------------------| r_work (start): 0.2510 rms_B_bonded: 2.96 r_work: 0.2371 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8790 Z= 0.146 Angle : 0.610 8.530 11954 Z= 0.301 Chirality : 0.039 0.146 1436 Planarity : 0.005 0.042 1396 Dihedral : 10.195 92.574 1830 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.11 % Allowed : 5.48 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.26), residues: 1012 helix: 1.54 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.82 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 760 TYR 0.015 0.002 TYR A 824 PHE 0.015 0.001 PHE B 411 TRP 0.016 0.002 TRP A 831 HIS 0.002 0.001 HIS A 734 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8778) covalent geometry : angle 0.60675 (11942) hydrogen bonds : bond 0.05223 ( 496) hydrogen bonds : angle 4.37999 ( 1452) Misc. bond : bond 0.00049 ( 8) link_BETA1-4 : bond 0.00571 ( 2) link_BETA1-4 : angle 1.80552 ( 6) link_NAG-ASN : bond 0.00526 ( 2) link_NAG-ASN : angle 2.32721 ( 6) *********************** 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 to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.231 Fit side-chains REVERT: A 663 MET cc_start: 0.9253 (tpp) cc_final: 0.9043 (tpp) REVERT: A 741 MET cc_start: 0.9436 (mmm) cc_final: 0.8985 (mmm) REVERT: A 776 MET cc_start: 0.9626 (ptp) cc_final: 0.9014 (ptp) REVERT: B 741 MET cc_start: 0.9452 (mmm) cc_final: 0.8990 (mmm) REVERT: B 776 MET cc_start: 0.9637 (ptp) cc_final: 0.9053 (ptp) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.0647 time to fit residues: 4.9809 Evaluate side-chains 43 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.054026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.043738 restraints weight = 26503.410| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 2.99 r_work: 0.2360 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8790 Z= 0.159 Angle : 0.544 7.326 11954 Z= 0.271 Chirality : 0.039 0.150 1436 Planarity : 0.005 0.046 1396 Dihedral : 9.079 82.607 1830 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.89 % Allowed : 6.15 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.27), residues: 1012 helix: 2.04 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.98 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 760 TYR 0.011 0.001 TYR B 486 PHE 0.010 0.001 PHE B 411 TRP 0.012 0.001 TRP A 831 HIS 0.001 0.000 HIS B 819 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8778) covalent geometry : angle 0.54082 (11942) hydrogen bonds : bond 0.04680 ( 496) hydrogen bonds : angle 4.06377 ( 1452) Misc. bond : bond 0.00060 ( 8) link_BETA1-4 : bond 0.00589 ( 2) link_BETA1-4 : angle 1.33675 ( 6) link_NAG-ASN : bond 0.00031 ( 2) link_NAG-ASN : angle 2.32356 ( 6) *********************** 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 53 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.275 Fit side-chains REVERT: A 741 MET cc_start: 0.9308 (mmm) cc_final: 0.8769 (mmm) REVERT: B 663 MET cc_start: 0.9367 (tpt) cc_final: 0.9144 (tpp) REVERT: B 741 MET cc_start: 0.9316 (mmm) cc_final: 0.8800 (mmm) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.1061 time to fit residues: 7.6077 Evaluate side-chains 47 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR 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 67 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.054883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.044588 restraints weight = 26753.127| |-----------------------------------------------------------------------------| r_work (start): 0.2529 rms_B_bonded: 3.03 r_work: 0.2385 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8790 Z= 0.124 Angle : 0.513 8.178 11954 Z= 0.253 Chirality : 0.038 0.127 1436 Planarity : 0.005 0.047 1396 Dihedral : 8.661 76.262 1830 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.78 % Allowed : 7.27 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.27), residues: 1012 helix: 2.24 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.75 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 603 TYR 0.010 0.001 TYR A 486 PHE 0.010 0.001 PHE B 471 TRP 0.018 0.001 TRP A 662 HIS 0.001 0.000 HIS B 819 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8778) covalent geometry : angle 0.51037 (11942) hydrogen bonds : bond 0.04125 ( 496) hydrogen bonds : angle 3.88228 ( 1452) Misc. bond : bond 0.00042 ( 8) link_BETA1-4 : bond 0.00582 ( 2) link_BETA1-4 : angle 1.26565 ( 6) link_NAG-ASN : bond 0.00016 ( 2) link_NAG-ASN : angle 2.09079 ( 6) *********************** 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 to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 776 MET cc_start: 0.9582 (ptp) cc_final: 0.9034 (ptp) REVERT: A 853 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8977 (t) REVERT: B 663 MET cc_start: 0.9329 (tpt) cc_final: 0.9102 (tpp) outliers start: 7 outliers final: 2 residues processed: 51 average time/residue: 0.0823 time to fit residues: 6.2772 Evaluate side-chains 47 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 872 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 1.9990 chunk 100 optimal weight: 0.0570 chunk 14 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.055037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.044755 restraints weight = 26467.026| |-----------------------------------------------------------------------------| r_work (start): 0.2534 rms_B_bonded: 2.96 r_work: 0.2394 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8790 Z= 0.125 Angle : 0.508 9.115 11954 Z= 0.248 Chirality : 0.038 0.120 1436 Planarity : 0.005 0.047 1396 Dihedral : 8.496 70.893 1830 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.56 % Allowed : 8.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.27), residues: 1012 helix: 2.33 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -0.72 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 760 TYR 0.010 0.001 TYR B 486 PHE 0.012 0.001 PHE B 526 TRP 0.021 0.001 TRP A 662 HIS 0.001 0.000 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8778) covalent geometry : angle 0.50526 (11942) hydrogen bonds : bond 0.04050 ( 496) hydrogen bonds : angle 3.82494 ( 1452) Misc. bond : bond 0.00037 ( 8) link_BETA1-4 : bond 0.00527 ( 2) link_BETA1-4 : angle 1.26652 ( 6) link_NAG-ASN : bond 0.00069 ( 2) link_NAG-ASN : angle 2.12799 ( 6) *********************** 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 53 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 664 MET cc_start: 0.9251 (mtm) cc_final: 0.8787 (mtm) REVERT: B 853 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.9043 (t) outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 0.0868 time to fit residues: 6.5361 Evaluate side-chains 47 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR 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 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 60 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.0020 chunk 20 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN B 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.055753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.045506 restraints weight = 26208.961| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 2.97 r_work: 0.2416 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8790 Z= 0.108 Angle : 0.505 10.045 11954 Z= 0.245 Chirality : 0.038 0.191 1436 Planarity : 0.004 0.047 1396 Dihedral : 8.352 67.623 1830 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.12 % Allowed : 8.61 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.27), residues: 1012 helix: 2.44 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.58 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 760 TYR 0.009 0.001 TYR B 486 PHE 0.011 0.001 PHE A 471 TRP 0.025 0.001 TRP B 662 HIS 0.001 0.000 HIS A 703 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8778) covalent geometry : angle 0.50236 (11942) hydrogen bonds : bond 0.03850 ( 496) hydrogen bonds : angle 3.80265 ( 1452) Misc. bond : bond 0.00025 ( 8) link_BETA1-4 : bond 0.00494 ( 2) link_BETA1-4 : angle 1.19500 ( 6) link_NAG-ASN : bond 0.00008 ( 2) link_NAG-ASN : angle 2.06885 ( 6) *********************** 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 56 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 853 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.9007 (t) REVERT: B 663 MET cc_start: 0.9449 (tpp) cc_final: 0.9105 (tpp) REVERT: B 664 MET cc_start: 0.9335 (mtm) cc_final: 0.8849 (mtm) REVERT: B 853 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.9019 (t) outliers start: 10 outliers final: 2 residues processed: 54 average time/residue: 0.0906 time to fit residues: 7.1084 Evaluate side-chains 48 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 55 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.054367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.044079 restraints weight = 27003.192| |-----------------------------------------------------------------------------| r_work (start): 0.2522 rms_B_bonded: 2.98 r_work: 0.2382 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8790 Z= 0.143 Angle : 0.527 11.024 11954 Z= 0.256 Chirality : 0.038 0.120 1436 Planarity : 0.004 0.047 1396 Dihedral : 8.251 63.569 1830 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.67 % Allowed : 8.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.27), residues: 1012 helix: 2.44 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.65 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 490 TYR 0.010 0.001 TYR B 486 PHE 0.010 0.001 PHE A 471 TRP 0.015 0.001 TRP A 662 HIS 0.001 0.000 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8778) covalent geometry : angle 0.52493 (11942) hydrogen bonds : bond 0.04165 ( 496) hydrogen bonds : angle 3.83749 ( 1452) Misc. bond : bond 0.00048 ( 8) link_BETA1-4 : bond 0.00500 ( 2) link_BETA1-4 : angle 1.17766 ( 6) link_NAG-ASN : bond 0.00097 ( 2) link_NAG-ASN : angle 1.98086 ( 6) *********************** 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 54 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.9462 (mtm) cc_final: 0.8942 (mtm) REVERT: A 853 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8963 (t) REVERT: B 663 MET cc_start: 0.9414 (tpp) cc_final: 0.9027 (tpp) REVERT: B 664 MET cc_start: 0.9364 (mtm) cc_final: 0.8898 (mtm) REVERT: B 853 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.9006 (t) outliers start: 6 outliers final: 2 residues processed: 52 average time/residue: 0.0883 time to fit residues: 6.6260 Evaluate side-chains 48 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 853 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 70 optimal weight: 0.0770 chunk 99 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.054932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.044569 restraints weight = 26170.864| |-----------------------------------------------------------------------------| r_work (start): 0.2507 rms_B_bonded: 3.10 r_work: 0.2371 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8790 Z= 0.113 Angle : 0.503 8.655 11954 Z= 0.246 Chirality : 0.037 0.118 1436 Planarity : 0.004 0.046 1396 Dihedral : 8.146 61.293 1830 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.89 % Allowed : 8.95 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.27), residues: 1012 helix: 2.52 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.41 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 490 TYR 0.009 0.001 TYR A 486 PHE 0.010 0.001 PHE A 471 TRP 0.026 0.001 TRP A 662 HIS 0.001 0.000 HIS A 703 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8778) covalent geometry : angle 0.50066 (11942) hydrogen bonds : bond 0.03869 ( 496) hydrogen bonds : angle 3.80698 ( 1452) Misc. bond : bond 0.00033 ( 8) link_BETA1-4 : bond 0.00519 ( 2) link_BETA1-4 : angle 1.13001 ( 6) link_NAG-ASN : bond 0.00006 ( 2) link_NAG-ASN : angle 1.88650 ( 6) *********************** 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 54 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.9407 (mtm) cc_final: 0.8891 (mtm) REVERT: A 853 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8808 (t) REVERT: B 664 MET cc_start: 0.9337 (mtm) cc_final: 0.8823 (mtm) REVERT: B 853 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8814 (t) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.0840 time to fit residues: 6.4361 Evaluate side-chains 51 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain B residue 418 SER 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 52 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.054511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.044179 restraints weight = 26522.878| |-----------------------------------------------------------------------------| r_work (start): 0.2500 rms_B_bonded: 3.11 r_work: 0.2363 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8790 Z= 0.124 Angle : 0.514 11.327 11954 Z= 0.249 Chirality : 0.037 0.117 1436 Planarity : 0.004 0.046 1396 Dihedral : 8.097 59.452 1830 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.56 % Allowed : 9.40 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.27), residues: 1012 helix: 2.52 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.51 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 490 TYR 0.009 0.001 TYR B 486 PHE 0.010 0.001 PHE A 471 TRP 0.023 0.002 TRP A 662 HIS 0.001 0.000 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8778) covalent geometry : angle 0.51160 (11942) hydrogen bonds : bond 0.03937 ( 496) hydrogen bonds : angle 3.80510 ( 1452) Misc. bond : bond 0.00037 ( 8) link_BETA1-4 : bond 0.00481 ( 2) link_BETA1-4 : angle 1.08967 ( 6) link_NAG-ASN : bond 0.00031 ( 2) link_NAG-ASN : angle 1.85712 ( 6) *********************** 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 52 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.9398 (mtm) cc_final: 0.8901 (mtm) REVERT: A 853 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8814 (t) REVERT: B 663 MET cc_start: 0.9338 (tpp) cc_final: 0.9007 (tpp) REVERT: B 664 MET cc_start: 0.9368 (mtm) cc_final: 0.8873 (mtm) REVERT: B 853 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8818 (t) outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 0.0821 time to fit residues: 6.2364 Evaluate side-chains 48 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 853 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.054936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.044913 restraints weight = 26507.862| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 2.98 r_work: 0.2414 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8790 Z= 0.122 Angle : 0.510 10.281 11954 Z= 0.247 Chirality : 0.037 0.117 1436 Planarity : 0.004 0.046 1396 Dihedral : 8.058 58.831 1830 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.89 % Allowed : 9.06 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.27), residues: 1012 helix: 2.54 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.53 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 490 TYR 0.009 0.001 TYR A 486 PHE 0.010 0.001 PHE B 471 TRP 0.021 0.001 TRP A 662 HIS 0.001 0.000 HIS A 703 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8778) covalent geometry : angle 0.50770 (11942) hydrogen bonds : bond 0.03902 ( 496) hydrogen bonds : angle 3.79381 ( 1452) Misc. bond : bond 0.00037 ( 8) link_BETA1-4 : bond 0.00499 ( 2) link_BETA1-4 : angle 1.05528 ( 6) link_NAG-ASN : bond 0.00009 ( 2) link_NAG-ASN : angle 1.77841 ( 6) ********************** 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 52 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.9437 (mtm) cc_final: 0.8998 (mtm) REVERT: A 853 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8960 (t) REVERT: B 663 MET cc_start: 0.9311 (tpp) cc_final: 0.8971 (tpp) REVERT: B 664 MET cc_start: 0.9343 (mtm) cc_final: 0.8929 (mtm) REVERT: B 853 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8974 (t) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.0905 time to fit residues: 6.8472 Evaluate side-chains 50 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain B residue 418 SER 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 81 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.054997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.045100 restraints weight = 26694.364| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 2.93 r_work: 0.2417 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8790 Z= 0.119 Angle : 0.503 10.488 11954 Z= 0.244 Chirality : 0.037 0.116 1436 Planarity : 0.004 0.046 1396 Dihedral : 7.932 58.795 1830 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.67 % Allowed : 9.28 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.27), residues: 1012 helix: 2.61 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -0.54 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 760 TYR 0.009 0.001 TYR B 486 PHE 0.010 0.001 PHE B 471 TRP 0.020 0.001 TRP A 662 HIS 0.001 0.000 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8778) covalent geometry : angle 0.50156 (11942) hydrogen bonds : bond 0.03836 ( 496) hydrogen bonds : angle 3.76881 ( 1452) Misc. bond : bond 0.00036 ( 8) link_BETA1-4 : bond 0.00454 ( 2) link_BETA1-4 : angle 0.98773 ( 6) link_NAG-ASN : bond 0.00017 ( 2) link_NAG-ASN : angle 1.67721 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1609.99 seconds wall clock time: 28 minutes 21.11 seconds (1701.11 seconds total)