Starting phenix.real_space_refine on Thu Feb 13 17:19:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tya_26171/02_2025/7tya_26171.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tya_26171/02_2025/7tya_26171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tya_26171/02_2025/7tya_26171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tya_26171/02_2025/7tya_26171.map" model { file = "/net/cci-nas-00/data/ceres_data/7tya_26171/02_2025/7tya_26171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tya_26171/02_2025/7tya_26171.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 5794 2.51 5 N 1312 2.21 5 O 1473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.83, per 1000 atoms: 0.68 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: 2.38 Conformation dependent library (CDL) restraints added in 913.8 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: 0.80 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: 2.32 Time building geometry restraints manager: 2.67 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: 0.04 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: 2.020 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.160 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.690 ------------------------------------------------------------------------------- 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 8778 Z= 0.949 Angle : 1.808 15.351 11942 Z= 1.359 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (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 TRP 0.024 0.003 TRP A 492 HIS 0.005 0.001 HIS A 834 PHE 0.016 0.002 PHE A 464 TYR 0.012 0.003 TYR B 393 ARG 0.005 0.001 ARG A 730 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.916 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: 0.2308 time to fit residues: 23.9886 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 : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.2799 r_free = 0.2799 target = 0.054943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.044554 restraints weight = 26344.498| |-----------------------------------------------------------------------------| r_work (start): 0.2504 rms_B_bonded: 2.95 r_work: 0.2364 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8778 Z= 0.223 Angle : 0.609 8.621 11942 Z= 0.301 Chirality : 0.039 0.148 1436 Planarity : 0.005 0.042 1396 Dihedral : 10.176 92.457 1830 Min Nonbonded Distance : 2.580 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 1012 helix: 1.54 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.83 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 831 HIS 0.002 0.001 HIS B 734 PHE 0.015 0.001 PHE A 411 TYR 0.014 0.002 TYR A 824 ARG 0.004 0.001 ARG A 760 *********************** 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 : 0.874 Fit side-chains REVERT: A 663 MET cc_start: 0.9248 (tpp) cc_final: 0.9041 (tpp) REVERT: A 741 MET cc_start: 0.9436 (mmm) cc_final: 0.8970 (mmm) REVERT: A 776 MET cc_start: 0.9631 (ptp) cc_final: 0.9048 (ptp) REVERT: B 741 MET cc_start: 0.9451 (mmm) cc_final: 0.8987 (mmm) REVERT: B 776 MET cc_start: 0.9634 (ptp) cc_final: 0.9067 (ptp) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.1524 time to fit residues: 11.7076 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 : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.2847 r_free = 0.2847 target = 0.056435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.046070 restraints weight = 26334.000| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 3.01 r_work: 0.2413 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8778 Z= 0.152 Angle : 0.504 7.259 11942 Z= 0.255 Chirality : 0.038 0.152 1436 Planarity : 0.005 0.046 1396 Dihedral : 8.928 82.194 1830 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.27), residues: 1012 helix: 2.13 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -0.79 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 492 HIS 0.001 0.000 HIS B 734 PHE 0.012 0.001 PHE A 411 TYR 0.011 0.001 TYR A 486 ARG 0.003 0.000 ARG A 760 *********************** 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 50 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.945 Fit side-chains REVERT: A 741 MET cc_start: 0.9347 (mmm) cc_final: 0.8818 (mmm) REVERT: B 741 MET cc_start: 0.9357 (mmm) cc_final: 0.8834 (mmm) REVERT: B 776 MET cc_start: 0.9615 (ptp) cc_final: 0.9160 (ptp) outliers start: 8 outliers final: 2 residues processed: 48 average time/residue: 0.1796 time to fit residues: 13.4389 Evaluate side-chains 42 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain B residue 555 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 90 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.2804 r_free = 0.2804 target = 0.054374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.044086 restraints weight = 26587.747| |-----------------------------------------------------------------------------| r_work (start): 0.2516 rms_B_bonded: 3.03 r_work: 0.2373 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8778 Z= 0.243 Angle : 0.540 10.676 11942 Z= 0.264 Chirality : 0.038 0.129 1436 Planarity : 0.005 0.046 1396 Dihedral : 8.637 76.182 1830 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.27), residues: 1012 helix: 2.20 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.88 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 662 HIS 0.001 0.000 HIS A 819 PHE 0.009 0.001 PHE A 471 TYR 0.011 0.001 TYR A 486 ARG 0.003 0.000 ARG A 490 *********************** 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 46 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 663 MET cc_start: 0.9443 (tpt) cc_final: 0.9201 (tpp) outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 0.2288 time to fit residues: 14.9065 Evaluate side-chains 44 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.2815 r_free = 0.2815 target = 0.054852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.044604 restraints weight = 26319.980| |-----------------------------------------------------------------------------| r_work (start): 0.2527 rms_B_bonded: 3.02 r_work: 0.2385 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8778 Z= 0.211 Angle : 0.510 8.548 11942 Z= 0.251 Chirality : 0.038 0.124 1436 Planarity : 0.005 0.047 1396 Dihedral : 8.509 70.665 1830 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.89 % Allowed : 7.61 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.27), residues: 1012 helix: 2.34 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -0.71 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 662 HIS 0.001 0.000 HIS B 819 PHE 0.010 0.001 PHE A 471 TYR 0.010 0.001 TYR B 486 ARG 0.003 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.9329 (mtm) cc_final: 0.8902 (mtm) REVERT: A 776 MET cc_start: 0.9545 (ptt) cc_final: 0.9338 (ptp) REVERT: A 853 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.9008 (t) REVERT: B 663 MET cc_start: 0.9419 (tpt) cc_final: 0.9142 (tpp) REVERT: B 664 MET cc_start: 0.9288 (mtm) cc_final: 0.8789 (mtm) REVERT: B 776 MET cc_start: 0.9505 (ptt) cc_final: 0.9297 (ptp) REVERT: B 853 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.9034 (t) outliers start: 8 outliers final: 2 residues processed: 55 average time/residue: 0.1938 time to fit residues: 15.9765 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 : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 853 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.0370 chunk 18 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.055432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.045128 restraints weight = 26306.456| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 3.02 r_work: 0.2403 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8778 Z= 0.173 Angle : 0.497 6.785 11942 Z= 0.244 Chirality : 0.038 0.206 1436 Planarity : 0.005 0.047 1396 Dihedral : 8.369 66.931 1830 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.89 % Allowed : 8.72 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.28), residues: 1012 helix: 2.44 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -0.57 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 662 HIS 0.001 0.000 HIS B 703 PHE 0.012 0.001 PHE B 526 TYR 0.010 0.001 TYR B 486 ARG 0.002 0.000 ARG A 760 *********************** 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 : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.9346 (mtm) cc_final: 0.8936 (mtm) REVERT: A 843 CYS cc_start: 0.9189 (m) cc_final: 0.8982 (m) REVERT: A 853 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.8997 (t) REVERT: B 663 MET cc_start: 0.9379 (tpt) cc_final: 0.9106 (tpp) REVERT: B 664 MET cc_start: 0.9316 (mtm) cc_final: 0.8883 (mtm) REVERT: B 853 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9028 (t) outliers start: 8 outliers final: 0 residues processed: 54 average time/residue: 0.2011 time to fit residues: 16.3148 Evaluate side-chains 47 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain B residue 853 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.0040 chunk 44 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.0050 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.055990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.045765 restraints weight = 26503.639| |-----------------------------------------------------------------------------| r_work (start): 0.2557 rms_B_bonded: 3.03 r_work: 0.2415 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8778 Z= 0.157 Angle : 0.491 7.133 11942 Z= 0.242 Chirality : 0.037 0.124 1436 Planarity : 0.004 0.048 1396 Dihedral : 8.170 63.251 1830 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.67 % Allowed : 8.61 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.28), residues: 1012 helix: 2.51 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 831 HIS 0.001 0.000 HIS A 703 PHE 0.010 0.001 PHE B 471 TYR 0.010 0.001 TYR B 486 ARG 0.002 0.000 ARG B 760 *********************** 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 57 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.9296 (mtm) cc_final: 0.8928 (mtm) REVERT: A 853 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8956 (t) REVERT: B 663 MET cc_start: 0.9360 (tpt) cc_final: 0.9044 (tpp) REVERT: B 853 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8981 (t) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.2004 time to fit residues: 16.3964 Evaluate side-chains 52 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 555 TYR 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 51 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 100 optimal weight: 0.0570 chunk 65 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.2848 r_free = 0.2848 target = 0.055986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.045849 restraints weight = 26543.376| |-----------------------------------------------------------------------------| r_work (start): 0.2566 rms_B_bonded: 3.01 r_work: 0.2426 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8778 Z= 0.156 Angle : 0.491 10.827 11942 Z= 0.241 Chirality : 0.037 0.116 1436 Planarity : 0.004 0.046 1396 Dihedral : 7.965 59.717 1830 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.67 % Allowed : 8.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.28), residues: 1012 helix: 2.55 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.42 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 662 HIS 0.001 0.000 HIS B 703 PHE 0.010 0.001 PHE B 471 TYR 0.010 0.001 TYR A 486 ARG 0.002 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 663 MET cc_start: 0.9323 (tpp) cc_final: 0.9008 (tpp) REVERT: A 664 MET cc_start: 0.9258 (mtm) cc_final: 0.8917 (mtm) REVERT: A 853 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8968 (t) REVERT: B 663 MET cc_start: 0.9353 (tpt) cc_final: 0.9003 (tpp) REVERT: B 853 THR cc_start: 0.9237 (OUTLIER) cc_final: 0.8997 (t) outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 0.2205 time to fit residues: 17.4724 Evaluate side-chains 50 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.2776 r_free = 0.2776 target = 0.053945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.043655 restraints weight = 26676.185| |-----------------------------------------------------------------------------| r_work (start): 0.2484 rms_B_bonded: 3.12 r_work: 0.2345 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 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 : 0.004 0.044 8778 Z= 0.237 Angle : 0.521 9.790 11942 Z= 0.255 Chirality : 0.038 0.118 1436 Planarity : 0.004 0.047 1396 Dihedral : 8.071 58.841 1830 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.68 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.27), residues: 1012 helix: 2.52 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.48 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 662 HIS 0.001 0.000 HIS A 703 PHE 0.009 0.001 PHE B 471 TYR 0.010 0.001 TYR B 486 ARG 0.002 0.000 ARG B 760 *********************** 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 53 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 663 MET cc_start: 0.9336 (tpp) cc_final: 0.9135 (tpp) REVERT: A 664 MET cc_start: 0.9283 (mtm) cc_final: 0.8877 (mtm) REVERT: A 853 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8829 (t) REVERT: B 853 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8847 (t) outliers start: 6 outliers final: 2 residues processed: 51 average time/residue: 0.2084 time to fit residues: 15.8107 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 : 0.911 ------------------------------------------------------------------------------- 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 69 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 86 optimal weight: 0.0370 chunk 91 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.054995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.044563 restraints weight = 26670.538| |-----------------------------------------------------------------------------| r_work (start): 0.2509 rms_B_bonded: 3.13 r_work: 0.2367 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8778 Z= 0.193 Angle : 0.509 9.298 11942 Z= 0.249 Chirality : 0.038 0.117 1436 Planarity : 0.004 0.047 1396 Dihedral : 8.022 57.770 1830 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.56 % Allowed : 8.72 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.27), residues: 1012 helix: 2.53 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.53 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 662 HIS 0.001 0.000 HIS A 703 PHE 0.010 0.001 PHE B 471 TYR 0.009 0.001 TYR B 486 ARG 0.002 0.000 ARG A 760 ********************** 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 49 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.9252 (mtm) cc_final: 0.8831 (mtm) REVERT: A 853 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8757 (t) REVERT: B 853 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8780 (t) outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 0.2011 time to fit residues: 14.3633 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 : 0.959 ------------------------------------------------------------------------------- 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 74 optimal weight: 4.9990 chunk 100 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.055058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.044944 restraints weight = 26809.345| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 3.02 r_work: 0.2405 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8778 Z= 0.183 Angle : 0.499 7.177 11942 Z= 0.245 Chirality : 0.037 0.116 1436 Planarity : 0.004 0.046 1396 Dihedral : 7.964 59.918 1830 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.56 % Allowed : 8.72 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.27), residues: 1012 helix: 2.55 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.55 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 662 HIS 0.001 0.000 HIS A 703 PHE 0.010 0.001 PHE B 471 TYR 0.009 0.001 TYR B 486 ARG 0.002 0.000 ARG A 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3233.41 seconds wall clock time: 58 minutes 28.90 seconds (3508.90 seconds total)