Starting phenix.real_space_refine on Thu Jul 2 16:03:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tya_26171/07_2026/7tya_26171.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tya_26171/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7tya_26171/07_2026/7tya_26171.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tya_26171/07_2026/7tya_26171.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tya_26171/07_2026/7tya_26171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tya_26171/07_2026/7tya_26171.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tya_26171/07_2026/7tya_26171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tya_26171/07_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-6108/lib/python3.11/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 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 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: 1.95, per 1000 atoms: 0.23 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: 0.98 Conformation dependent library (CDL) restraints added in 303.7 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: 0.24 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: 1.34 Time building geometry restraints manager: 1.18 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: 4856 25.61 - 51.21: 193 51.21 - 76.82: 33 76.82 - 102.42: 6 102.42 - 128.02: 2 Dihedral angle restraints: 5090 sinusoidal: 2122 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=" C VAL A 822 " pdb=" N VAL A 822 " pdb=" CA VAL A 822 " pdb=" CB VAL A 822 " ideal model delta harmonic sigma weight residual -122.00 -131.80 9.80 0 2.50e+00 1.60e-01 1.54e+01 ... (remaining 5087 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: 0.02 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: 2.820 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.390 Find NCS groups from input model: 0.070 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 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 : 14.758 128.024 3170 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/Z covalent geometry : bond 0.01493 / 1.06 ( 8778) covalent geometry : angle 1.80783 / 1.36 (11942) hydrogen bonds : bond 0.24649 / 15.91 ( 496) hydrogen bonds : angle 8.33089 / 5.90 ( 1452) Misc. bond : bond 0.10089 / 5.18 ( 8) link_BETA1-4 : bond 0.00578 / 0.29 ( 2) link_BETA1-4 : angle 1.07894 / 0.78 ( 6) link_NAG-ASN : bond 0.00299 / 0.15 ( 2) link_NAG-ASN : angle 7.32054 / 3.78 ( 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 : 0.330 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: 0.0930 time to fit residues: 9.8352 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 : 0.329 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.055130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.044725 restraints weight = 26438.959| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 2.96 r_work: 0.2369 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8790 Z= 0.143 Angle : 0.611 8.594 11954 Z= 0.301 Chirality : 0.039 0.144 1436 Planarity : 0.005 0.041 1396 Dihedral : 10.974 101.545 1280 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.72 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: 1.11 (0.26), residues: 1012 helix: 1.52 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.84 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 760 TYR 0.013 0.002 TYR A 824 PHE 0.015 0.001 PHE A 411 TRP 0.016 0.002 TRP A 831 HIS 0.002 0.001 HIS B 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8778) covalent geometry : angle 0.60732 / 0.30 (11942) hydrogen bonds : bond 0.05351 / 3.60 ( 496) hydrogen bonds : angle 4.39207 / 3.33 ( 1452) Misc. bond : bond 0.00062 / 0.03 ( 8) link_BETA1-4 : bond 0.00521 / 0.26 ( 2) link_BETA1-4 : angle 1.74026 / 0.94 ( 6) link_NAG-ASN : bond 0.00246 / 0.12 ( 2) link_NAG-ASN : angle 2.34051 / 1.18 ( 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 : 0.311 Fit side-chains REVERT: A 663 MET cc_start: 0.9237 (tpp) cc_final: 0.9031 (tpp) REVERT: A 741 MET cc_start: 0.9438 (mmm) cc_final: 0.8985 (mmm) REVERT: A 776 MET cc_start: 0.9630 (ptp) cc_final: 0.9030 (ptp) REVERT: B 741 MET cc_start: 0.9458 (mmm) cc_final: 0.8993 (mmm) REVERT: B 776 MET cc_start: 0.9640 (ptp) cc_final: 0.9066 (ptp) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.0746 time to fit residues: 5.5356 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 : 0.271 ------------------------------------------------------------------------------- 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: 0.0770 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.053642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.043311 restraints weight = 26649.100| |-----------------------------------------------------------------------------| r_work (start): 0.2487 rms_B_bonded: 3.00 r_work: 0.2347 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8790 Z= 0.180 Angle : 0.570 7.358 11954 Z= 0.279 Chirality : 0.039 0.153 1436 Planarity : 0.005 0.046 1396 Dihedral : 9.838 102.607 1280 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.89 % Allowed : 6.38 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.67 (0.27), residues: 1012 helix: 2.01 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -0.93 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 760 TYR 0.012 0.001 TYR B 486 PHE 0.010 0.001 PHE B 411 TRP 0.012 0.001 TRP B 492 HIS 0.001 0.000 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 8778) covalent geometry : angle 0.56762 / 0.28 (11942) hydrogen bonds : bond 0.04788 / 3.21 ( 496) hydrogen bonds : angle 4.07711 / 3.11 ( 1452) Misc. bond : bond 0.00062 / 0.03 ( 8) link_BETA1-4 : bond 0.00553 / 0.28 ( 2) link_BETA1-4 : angle 1.27349 / 0.66 ( 6) link_NAG-ASN : bond 0.00093 / 0.05 ( 2) link_NAG-ASN : angle 2.18497 / 1.17 ( 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 : 0.289 Fit side-chains REVERT: A 741 MET cc_start: 0.9281 (mmm) cc_final: 0.8732 (mmm) REVERT: B 741 MET cc_start: 0.9290 (mmm) cc_final: 0.8782 (mmm) outliers start: 8 outliers final: 2 residues processed: 51 average time/residue: 0.1004 time to fit residues: 7.3594 Evaluate side-chains 45 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 872 VAL 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: 2.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.054286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.044014 restraints weight = 26959.498| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 3.04 r_work: 0.2371 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8790 Z= 0.136 Angle : 0.523 8.228 11954 Z= 0.258 Chirality : 0.038 0.129 1436 Planarity : 0.005 0.047 1396 Dihedral : 9.455 103.087 1280 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.22 % Allowed : 7.49 % 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 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: 1.91 (0.27), residues: 1012 helix: 2.18 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -0.81 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 760 TYR 0.010 0.001 TYR A 486 PHE 0.011 0.001 PHE A 411 TRP 0.018 0.001 TRP A 662 HIS 0.001 0.000 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8778) covalent geometry : angle 0.52094 / 0.26 (11942) hydrogen bonds : bond 0.04299 / 2.90 ( 496) hydrogen bonds : angle 3.92517 / 3.00 ( 1452) Misc. bond : bond 0.00048 / 0.02 ( 8) link_BETA1-4 : bond 0.00567 / 0.28 ( 2) link_BETA1-4 : angle 1.19394 / 0.62 ( 6) link_NAG-ASN : bond 0.00036 / 0.02 ( 2) link_NAG-ASN : angle 1.92096 / 1.08 ( 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 48 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 663 MET cc_start: 0.9440 (tpt) cc_final: 0.9169 (tpp) outliers start: 2 outliers final: 2 residues processed: 46 average time/residue: 0.0948 time to fit residues: 6.5510 Evaluate side-chains 46 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain B residue 555 TYR 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: 1.9990 chunk 14 optimal weight: 0.3980 chunk 93 optimal weight: 0.0060 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.053891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.043509 restraints weight = 26829.274| |-----------------------------------------------------------------------------| r_work (start): 0.2500 rms_B_bonded: 3.00 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: 0.8883 moved from start: 0.2489 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= 0.155 Angle : 0.532 10.956 11954 Z= 0.259 Chirality : 0.038 0.127 1436 Planarity : 0.005 0.047 1396 Dihedral : 9.249 103.491 1280 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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 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: 2.03 (0.27), residues: 1012 helix: 2.25 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 490 TYR 0.010 0.001 TYR B 486 PHE 0.011 0.001 PHE A 526 TRP 0.017 0.001 TRP A 662 HIS 0.001 0.000 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 8778) covalent geometry : angle 0.53003 / 0.26 (11942) hydrogen bonds : bond 0.04351 / 2.93 ( 496) hydrogen bonds : angle 3.89854 / 2.99 ( 1452) Misc. bond : bond 0.00055 / 0.03 ( 8) link_BETA1-4 : bond 0.00485 / 0.25 ( 2) link_BETA1-4 : angle 1.15009 / 0.59 ( 6) link_NAG-ASN : bond 0.00136 / 0.07 ( 2) link_NAG-ASN : angle 1.89626 / 1.11 ( 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 56 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 853 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.9010 (t) REVERT: B 663 MET cc_start: 0.9435 (tpt) cc_final: 0.9161 (tpp) REVERT: B 664 MET cc_start: 0.9317 (mtm) cc_final: 0.8827 (mtm) REVERT: B 776 MET cc_start: 0.9510 (ptt) cc_final: 0.9305 (ptp) REVERT: B 853 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.9026 (t) outliers start: 10 outliers final: 2 residues processed: 52 average time/residue: 0.0908 time to fit residues: 7.0679 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 : 0.368 ------------------------------------------------------------------------------- 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=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: 0.7980 chunk 14 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.054522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.044168 restraints weight = 26450.437| |-----------------------------------------------------------------------------| r_work (start): 0.2519 rms_B_bonded: 3.02 r_work: 0.2379 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2592 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= 0.127 Angle : 0.514 9.873 11954 Z= 0.252 Chirality : 0.038 0.194 1436 Planarity : 0.004 0.048 1396 Dihedral : 9.103 103.653 1280 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.89 % Allowed : 8.39 % 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 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: 2.12 (0.27), residues: 1012 helix: 2.33 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.67 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 603 TYR 0.009 0.001 TYR A 486 PHE 0.011 0.001 PHE A 471 TRP 0.019 0.001 TRP A 662 HIS 0.001 0.000 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 8778) covalent geometry : angle 0.51234 / 0.25 (11942) hydrogen bonds : bond 0.04076 / 2.75 ( 496) hydrogen bonds : angle 3.84271 / 2.94 ( 1452) Misc. bond : bond 0.00040 / 0.02 ( 8) link_BETA1-4 : bond 0.00439 / 0.22 ( 2) link_BETA1-4 : angle 1.10059 / 0.57 ( 6) link_NAG-ASN : bond 0.00065 / 0.03 ( 2) link_NAG-ASN : angle 1.76226 / 1.04 ( 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: 8 poor density : 48 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 663 MET cc_start: 0.9368 (tpp) cc_final: 0.9119 (tpp) REVERT: A 664 MET cc_start: 0.9315 (mtm) cc_final: 0.8999 (mtm) REVERT: A 853 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8974 (t) REVERT: B 663 MET cc_start: 0.9395 (tpt) cc_final: 0.9118 (tpp) REVERT: B 664 MET cc_start: 0.9342 (mtm) cc_final: 0.8890 (mtm) REVERT: B 853 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8994 (t) outliers start: 8 outliers final: 4 residues processed: 54 average time/residue: 0.0789 time to fit residues: 6.4705 Evaluate side-chains 51 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 5 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.2805 r_free = 0.2805 target = 0.054189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.043975 restraints weight = 27100.766| |-----------------------------------------------------------------------------| r_work (start): 0.2517 rms_B_bonded: 2.99 r_work: 0.2376 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2689 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= 0.138 Angle : 0.517 8.177 11954 Z= 0.253 Chirality : 0.038 0.121 1436 Planarity : 0.004 0.048 1396 Dihedral : 8.912 103.977 1280 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.78 % Allowed : 8.61 % 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 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: 686 sheet: None (None), residues: 0 loop : -0.57 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 760 TYR 0.009 0.001 TYR B 486 PHE 0.011 0.001 PHE A 471 TRP 0.013 0.001 TRP A 662 HIS 0.001 0.000 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8778) covalent geometry : angle 0.51554 / 0.25 (11942) hydrogen bonds : bond 0.04144 / 2.79 ( 496) hydrogen bonds : angle 3.84115 / 2.94 ( 1452) Misc. bond : bond 0.00047 / 0.02 ( 8) link_BETA1-4 : bond 0.00419 / 0.21 ( 2) link_BETA1-4 : angle 1.02243 / 0.53 ( 6) link_NAG-ASN : bond 0.00086 / 0.04 ( 2) link_NAG-ASN : angle 1.74621 / 1.02 ( 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: 7 poor density : 47 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.9290 (mtm) cc_final: 0.9013 (mtm) REVERT: A 853 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9001 (t) REVERT: B 663 MET cc_start: 0.9390 (tpt) cc_final: 0.9068 (tpp) REVERT: B 853 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.9012 (t) outliers start: 7 outliers final: 1 residues processed: 52 average time/residue: 0.0922 time to fit residues: 7.2487 Evaluate side-chains 48 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 853 THR 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 62 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.054340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.044234 restraints weight = 26493.980| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 2.96 r_work: 0.2385 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2764 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= 0.134 Angle : 0.520 11.721 11954 Z= 0.254 Chirality : 0.038 0.120 1436 Planarity : 0.004 0.048 1396 Dihedral : 8.786 104.118 1280 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.01 % Allowed : 8.39 % 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 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: 2.33 (0.27), residues: 1012 helix: 2.48 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.55 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 760 TYR 0.010 0.001 TYR A 486 PHE 0.011 0.001 PHE A 471 TRP 0.017 0.001 TRP A 662 HIS 0.001 0.000 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 8778) covalent geometry : angle 0.51793 / 0.25 (11942) hydrogen bonds : bond 0.04057 / 2.74 ( 496) hydrogen bonds : angle 3.83027 / 2.93 ( 1452) Misc. bond : bond 0.00046 / 0.02 ( 8) link_BETA1-4 : bond 0.00375 / 0.19 ( 2) link_BETA1-4 : angle 1.01222 / 0.52 ( 6) link_NAG-ASN : bond 0.00071 / 0.04 ( 2) link_NAG-ASN : angle 1.66095 / 0.99 ( 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 57 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 663 MET cc_start: 0.9352 (tpp) cc_final: 0.8992 (tpp) REVERT: A 664 MET cc_start: 0.9274 (mtm) cc_final: 0.9030 (mtm) REVERT: A 853 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8994 (t) REVERT: B 663 MET cc_start: 0.9389 (tpt) cc_final: 0.9050 (tpp) REVERT: B 853 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8999 (t) outliers start: 9 outliers final: 3 residues processed: 54 average time/residue: 0.0912 time to fit residues: 7.3174 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 : 0.371 ------------------------------------------------------------------------------- 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 555 TYR 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: 1.9990 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.054047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.043978 restraints weight = 26766.489| |-----------------------------------------------------------------------------| r_work (start): 0.2518 rms_B_bonded: 3.01 r_work: 0.2378 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8790 Z= 0.140 Angle : 0.521 10.306 11954 Z= 0.255 Chirality : 0.038 0.119 1436 Planarity : 0.004 0.048 1396 Dihedral : 8.669 104.288 1280 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.01 % Allowed : 8.61 % 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: 2.34 (0.27), residues: 1012 helix: 2.49 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.54 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 760 TYR 0.009 0.001 TYR B 486 PHE 0.010 0.001 PHE B 471 TRP 0.018 0.001 TRP A 662 HIS 0.001 0.000 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 8778) covalent geometry : angle 0.51965 / 0.25 (11942) hydrogen bonds : bond 0.04133 / 2.78 ( 496) hydrogen bonds : angle 3.84577 / 2.94 ( 1452) Misc. bond : bond 0.00050 / 0.03 ( 8) link_BETA1-4 : bond 0.00443 / 0.22 ( 2) link_BETA1-4 : angle 0.95840 / 0.50 ( 6) link_NAG-ASN : bond 0.00093 / 0.05 ( 2) link_NAG-ASN : angle 1.59178 / 0.96 ( 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 57 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 663 MET cc_start: 0.9336 (tpp) cc_final: 0.8979 (tpp) REVERT: A 664 MET cc_start: 0.9240 (mtm) cc_final: 0.9033 (mtm) REVERT: A 853 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8960 (t) REVERT: B 853 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8975 (t) outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 0.0812 time to fit residues: 6.7227 Evaluate side-chains 51 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 A residue 872 VAL 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 84 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.054852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.044521 restraints weight = 26560.898| |-----------------------------------------------------------------------------| r_work (start): 0.2506 rms_B_bonded: 3.12 r_work: 0.2364 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8790 Z= 0.119 Angle : 0.510 10.267 11954 Z= 0.250 Chirality : 0.038 0.116 1436 Planarity : 0.004 0.048 1396 Dihedral : 8.545 104.145 1280 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.78 % Allowed : 8.72 % Favored : 90.49 % 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: 2.38 (0.27), residues: 1012 helix: 2.53 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.56 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 760 TYR 0.009 0.001 TYR A 486 PHE 0.011 0.001 PHE B 471 TRP 0.015 0.001 TRP A 662 HIS 0.001 0.000 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 8778) covalent geometry : angle 0.50820 / 0.25 (11942) hydrogen bonds : bond 0.03944 / 2.66 ( 496) hydrogen bonds : angle 3.80818 / 2.92 ( 1452) Misc. bond : bond 0.00038 / 0.02 ( 8) link_BETA1-4 : bond 0.00481 / 0.24 ( 2) link_BETA1-4 : angle 0.95889 / 0.50 ( 6) link_NAG-ASN : bond 0.00022 / 0.01 ( 2) link_NAG-ASN : angle 1.53344 / 0.92 ( 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 51 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 663 MET cc_start: 0.9278 (tpp) cc_final: 0.8912 (tpp) REVERT: A 664 MET cc_start: 0.9207 (mtm) cc_final: 0.8931 (mtm) REVERT: A 853 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8738 (t) REVERT: B 853 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8737 (t) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 0.0843 time to fit residues: 6.3300 Evaluate side-chains 51 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 A residue 872 VAL 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: 0.7980 chunk 15 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 47 optimal weight: 0.0370 chunk 0 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.055558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.045548 restraints weight = 26682.454| |-----------------------------------------------------------------------------| r_work (start): 0.2567 rms_B_bonded: 3.02 r_work: 0.2429 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8790 Z= 0.110 Angle : 0.496 9.768 11954 Z= 0.244 Chirality : 0.037 0.116 1436 Planarity : 0.004 0.048 1396 Dihedral : 8.311 104.056 1280 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.89 % Allowed : 8.84 % 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: 2.41 (0.27), residues: 1012 helix: 2.56 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -0.60 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 603 TYR 0.009 0.001 TYR B 486 PHE 0.010 0.001 PHE B 471 TRP 0.016 0.001 TRP A 662 HIS 0.001 0.000 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 8778) covalent geometry : angle 0.49498 / 0.24 (11942) hydrogen bonds : bond 0.03748 / 2.51 ( 496) hydrogen bonds : angle 3.76709 / 2.90 ( 1452) Misc. bond : bond 0.00031 / 0.02 ( 8) link_BETA1-4 : bond 0.00421 / 0.21 ( 2) link_BETA1-4 : angle 0.90058 / 0.47 ( 6) link_NAG-ASN : bond 0.00005 / 0.00 ( 2) link_NAG-ASN : angle 1.51186 / 0.92 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1673.31 seconds wall clock time: 29 minutes 31.61 seconds (1771.61 seconds total)