Starting phenix.real_space_refine on Sun Jun 8 03:10:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tya_26171/06_2025/7tya_26171.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tya_26171/06_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_26171/06_2025/7tya_26171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tya_26171/06_2025/7tya_26171.map" model { file = "/net/cci-nas-00/data/ceres_data/7tya_26171/06_2025/7tya_26171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tya_26171/06_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-5710/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: 6.21, per 1000 atoms: 0.72 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: 2.65 Conformation dependent library (CDL) restraints added in 1.0 seconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... 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: 0.88 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: 2.14 Time building geometry restraints manager: 3.01 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: 2.480 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.770 Find NCS groups from input model: 0.140 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.333 8790 Z= 1.107 Angle : 1.815 15.351 11954 Z= 1.360 Chirality : 0.086 0.331 1436 Planarity : 0.013 0.255 1396 Dihedral : 14.955 128.024 3720 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.22 % Allowed : 3.24 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 2) link_NAG-ASN : angle 7.32054 ( 6) link_BETA1-4 : bond 0.00578 ( 2) link_BETA1-4 : angle 1.07894 ( 6) hydrogen bonds : bond 0.24649 ( 496) hydrogen bonds : angle 8.33089 ( 1452) covalent geometry : bond 0.01493 ( 8778) covalent geometry : angle 1.80783 (11942) Misc. bond : bond 0.10089 ( 8) *********************** 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 : 0.985 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: 0.2318 time to fit residues: 24.2464 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 : 1.096 ------------------------------------------------------------------------------- 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 = 0.054944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.044555 restraints weight = 26342.365| |-----------------------------------------------------------------------------| 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 8790 Z= 0.150 Angle : 0.611 8.621 11954 Z= 0.301 Chirality : 0.039 0.148 1436 Planarity : 0.005 0.042 1396 Dihedral : 10.175 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 2) link_NAG-ASN : angle 2.12656 ( 6) link_BETA1-4 : bond 0.00945 ( 2) link_BETA1-4 : angle 1.71880 ( 6) hydrogen bonds : bond 0.05330 ( 496) hydrogen bonds : angle 4.38774 ( 1452) covalent geometry : bond 0.00347 ( 8778) covalent geometry : angle 0.60869 (11942) Misc. bond : bond 0.00057 ( 8) *********************** 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 : 0.976 Fit side-chains REVERT: A 663 MET cc_start: 0.9248 (tpp) cc_final: 0.9040 (tpp) REVERT: A 741 MET cc_start: 0.9435 (mmm) cc_final: 0.8969 (mmm) REVERT: A 776 MET cc_start: 0.9632 (ptp) cc_final: 0.9047 (ptp) REVERT: B 741 MET cc_start: 0.9450 (mmm) cc_final: 0.8986 (mmm) REVERT: B 776 MET cc_start: 0.9635 (ptp) cc_final: 0.9068 (ptp) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.1621 time to fit residues: 12.3672 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 : 1.039 ------------------------------------------------------------------------------- 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: 4.9990 chunk 60 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 0.0030 overall best weight: 0.3990 ------------------------------------------------------------------------------- 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 = 0.056419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.046069 restraints weight = 26367.679| |-----------------------------------------------------------------------------| r_work (start): 0.2557 rms_B_bonded: 3.00 r_work: 0.2416 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8790 Z= 0.109 Angle : 0.509 7.258 11954 Z= 0.255 Chirality : 0.037 0.146 1436 Planarity : 0.005 0.046 1396 Dihedral : 8.907 81.881 1830 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.28 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: 1.81 (0.27), residues: 1012 helix: 2.14 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -0.80 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 492 HIS 0.001 0.000 HIS A 734 PHE 0.011 0.001 PHE A 411 TYR 0.011 0.001 TYR A 486 ARG 0.003 0.000 ARG B 760 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 2) link_NAG-ASN : angle 2.32281 ( 6) link_BETA1-4 : bond 0.00675 ( 2) link_BETA1-4 : angle 1.38558 ( 6) hydrogen bonds : bond 0.04181 ( 496) hydrogen bonds : angle 3.99985 ( 1452) covalent geometry : bond 0.00236 ( 8778) covalent geometry : angle 0.50536 (11942) Misc. bond : bond 0.00028 ( 8) *********************** 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 : 0.965 Fit side-chains REVERT: A 741 MET cc_start: 0.9313 (mmm) cc_final: 0.8795 (mmm) REVERT: B 741 MET cc_start: 0.9322 (mmm) cc_final: 0.8811 (mmm) outliers start: 8 outliers final: 2 residues processed: 48 average time/residue: 0.1731 time to fit residues: 13.1572 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 : 0.952 ------------------------------------------------------------------------------- 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: 0.0670 chunk 60 optimal weight: 0.1980 chunk 90 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.4120 ------------------------------------------------------------------------------- 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 = 0.2854 r_free = 0.2854 target = 0.056794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.046513 restraints weight = 26094.167| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 3.03 r_work: 0.2436 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8790 Z= 0.105 Angle : 0.501 9.692 11954 Z= 0.246 Chirality : 0.037 0.120 1436 Planarity : 0.005 0.046 1396 Dihedral : 8.471 76.046 1830 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.22 % Allowed : 7.83 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.99 (0.27), residues: 1012 helix: 2.28 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.80 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 662 HIS 0.001 0.000 HIS B 734 PHE 0.010 0.001 PHE B 411 TYR 0.010 0.001 TYR A 486 ARG 0.003 0.000 ARG A 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00022 ( 2) link_NAG-ASN : angle 2.19786 ( 6) link_BETA1-4 : bond 0.00517 ( 2) link_BETA1-4 : angle 1.31954 ( 6) hydrogen bonds : bond 0.03911 ( 496) hydrogen bonds : angle 3.84643 ( 1452) covalent geometry : bond 0.00233 ( 8778) covalent geometry : angle 0.49781 (11942) Misc. bond : bond 0.00022 ( 8) *********************** 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 50 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 843 CYS cc_start: 0.9189 (m) cc_final: 0.8975 (m) REVERT: B 663 MET cc_start: 0.9392 (tpt) cc_final: 0.9151 (tpp) outliers start: 2 outliers final: 0 residues processed: 48 average time/residue: 0.2035 time to fit residues: 14.5558 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 : 0.947 ------------------------------------------------------------------------------- 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: 0.5980 chunk 44 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.2835 r_free = 0.2835 target = 0.055623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.045411 restraints weight = 26098.348| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 3.00 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: 0.8791 moved from start: 0.2403 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= 0.125 Angle : 0.505 9.660 11954 Z= 0.247 Chirality : 0.038 0.120 1436 Planarity : 0.005 0.047 1396 Dihedral : 8.316 70.132 1830 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.12 % Allowed : 7.16 % Favored : 91.72 % 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: 2.12 (0.28), residues: 1012 helix: 2.37 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -0.68 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 662 HIS 0.001 0.000 HIS B 819 PHE 0.011 0.001 PHE A 526 TYR 0.012 0.001 TYR B 413 ARG 0.003 0.000 ARG B 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00028 ( 2) link_NAG-ASN : angle 2.21753 ( 6) link_BETA1-4 : bond 0.00526 ( 2) link_BETA1-4 : angle 1.24871 ( 6) hydrogen bonds : bond 0.04015 ( 496) hydrogen bonds : angle 3.82258 ( 1452) covalent geometry : bond 0.00294 ( 8778) covalent geometry : angle 0.50241 (11942) Misc. bond : bond 0.00037 ( 8) *********************** 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: 10 poor density : 49 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 843 CYS cc_start: 0.9208 (m) cc_final: 0.9000 (m) REVERT: A 853 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9044 (t) REVERT: B 663 MET cc_start: 0.9370 (tpt) cc_final: 0.9090 (tpp) REVERT: B 853 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9049 (t) outliers start: 10 outliers final: 2 residues processed: 53 average time/residue: 0.2455 time to fit residues: 20.3236 Evaluate side-chains 47 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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: 0.0070 chunk 18 optimal weight: 0.0770 chunk 42 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 49 optimal weight: 0.0010 chunk 8 optimal weight: 0.9990 overall best weight: 0.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN B 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.057217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.047043 restraints weight = 26041.579| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 3.03 r_work: 0.2452 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8790 Z= 0.099 Angle : 0.500 10.639 11954 Z= 0.244 Chirality : 0.037 0.210 1436 Planarity : 0.005 0.047 1396 Dihedral : 8.191 66.138 1830 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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 (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: 2.30 (0.28), residues: 1012 helix: 2.46 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.56 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 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 0.003 0.000 ARG A 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 2) link_NAG-ASN : angle 2.11306 ( 6) link_BETA1-4 : bond 0.00493 ( 2) link_BETA1-4 : angle 1.26468 ( 6) hydrogen bonds : bond 0.03610 ( 496) hydrogen bonds : angle 3.75367 ( 1452) covalent geometry : bond 0.00214 ( 8778) covalent geometry : angle 0.49676 (11942) Misc. bond : bond 0.00016 ( 8) *********************** 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 59 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 853 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9018 (t) REVERT: B 663 MET cc_start: 0.9359 (tpt) cc_final: 0.8996 (tpp) REVERT: B 853 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.9001 (t) outliers start: 8 outliers final: 0 residues processed: 57 average time/residue: 0.1947 time to fit residues: 17.3239 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 : 1.085 ------------------------------------------------------------------------------- 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: 0.3980 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.2852 r_free = 0.2852 target = 0.056313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.046176 restraints weight = 26585.419| |-----------------------------------------------------------------------------| r_work (start): 0.2571 rms_B_bonded: 3.04 r_work: 0.2431 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8790 Z= 0.113 Angle : 0.497 8.468 11954 Z= 0.243 Chirality : 0.037 0.115 1436 Planarity : 0.004 0.045 1396 Dihedral : 8.080 62.631 1830 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: 2.34 (0.28), residues: 1012 helix: 2.49 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -0.58 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 662 HIS 0.001 0.000 HIS A 703 PHE 0.009 0.001 PHE A 471 TYR 0.009 0.001 TYR B 486 ARG 0.002 0.000 ARG B 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00019 ( 2) link_NAG-ASN : angle 2.09417 ( 6) link_BETA1-4 : bond 0.00555 ( 2) link_BETA1-4 : angle 1.22647 ( 6) hydrogen bonds : bond 0.03758 ( 496) hydrogen bonds : angle 3.72881 ( 1452) covalent geometry : bond 0.00259 ( 8778) covalent geometry : angle 0.49403 (11942) Misc. bond : bond 0.00027 ( 8) *********************** 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 56 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.9438 (mtm) cc_final: 0.8939 (mtm) REVERT: A 853 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8985 (t) REVERT: B 663 MET cc_start: 0.9376 (tpt) cc_final: 0.8979 (tpp) REVERT: B 853 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8996 (t) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.1929 time to fit residues: 15.6012 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 : 0.945 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 74 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.2836 r_free = 0.2836 target = 0.055370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.045129 restraints weight = 26643.921| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 3.03 r_work: 0.2410 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2705 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= 0.129 Angle : 0.511 7.554 11954 Z= 0.251 Chirality : 0.038 0.117 1436 Planarity : 0.004 0.046 1396 Dihedral : 8.012 59.843 1830 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.67 % Allowed : 9.06 % 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 (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: 2.37 (0.27), residues: 1012 helix: 2.50 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.52 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 662 HIS 0.001 0.000 HIS A 703 PHE 0.009 0.001 PHE B 471 TYR 0.009 0.001 TYR A 486 ARG 0.002 0.000 ARG B 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00030 ( 2) link_NAG-ASN : angle 1.96842 ( 6) link_BETA1-4 : bond 0.00471 ( 2) link_BETA1-4 : angle 1.13095 ( 6) hydrogen bonds : bond 0.03955 ( 496) hydrogen bonds : angle 3.77366 ( 1452) covalent geometry : bond 0.00306 ( 8778) covalent geometry : angle 0.50847 (11942) Misc. bond : bond 0.00041 ( 8) *********************** 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 52 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.9452 (mtm) cc_final: 0.8980 (mtm) REVERT: A 776 MET cc_start: 0.9513 (ptp) cc_final: 0.9035 (ptp) REVERT: A 853 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8987 (t) REVERT: B 776 MET cc_start: 0.9517 (ptp) cc_final: 0.9044 (ptp) REVERT: B 853 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.9009 (t) outliers start: 6 outliers final: 2 residues processed: 50 average time/residue: 0.2051 time to fit residues: 15.2606 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 : 0.975 ------------------------------------------------------------------------------- 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: 0.0040 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 = 0.2844 r_free = 0.2844 target = 0.055616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.045479 restraints weight = 26549.617| |-----------------------------------------------------------------------------| r_work (start): 0.2557 rms_B_bonded: 3.03 r_work: 0.2417 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8790 Z= 0.117 Angle : 0.498 7.240 11954 Z= 0.245 Chirality : 0.037 0.115 1436 Planarity : 0.004 0.045 1396 Dihedral : 7.888 57.491 1830 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.67 % Allowed : 9.17 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.42 (0.27), residues: 1012 helix: 2.55 (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 0.023 0.001 TRP A 662 HIS 0.001 0.000 HIS B 703 PHE 0.009 0.001 PHE B 471 TYR 0.009 0.001 TYR B 486 ARG 0.002 0.000 ARG A 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00013 ( 2) link_NAG-ASN : angle 1.90858 ( 6) link_BETA1-4 : bond 0.00521 ( 2) link_BETA1-4 : angle 1.10949 ( 6) hydrogen bonds : bond 0.03804 ( 496) hydrogen bonds : angle 3.75642 ( 1452) covalent geometry : bond 0.00271 ( 8778) covalent geometry : angle 0.49586 (11942) Misc. bond : bond 0.00035 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 663 MET cc_start: 0.8998 (tpp) cc_final: 0.8768 (mmm) REVERT: A 664 MET cc_start: 0.9429 (mtm) cc_final: 0.8986 (mtm) REVERT: A 853 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8966 (t) REVERT: B 853 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8989 (t) outliers start: 6 outliers final: 2 residues processed: 50 average time/residue: 0.2934 time to fit residues: 22.8607 Evaluate side-chains 49 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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: 0.7980 chunk 58 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.2850 r_free = 0.2850 target = 0.056011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.045892 restraints weight = 26431.313| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 3.04 r_work: 0.2430 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8790 Z= 0.114 Angle : 0.496 7.139 11954 Z= 0.244 Chirality : 0.037 0.115 1436 Planarity : 0.004 0.046 1396 Dihedral : 7.777 55.414 1830 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.45 % Allowed : 9.28 % 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 (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: 2.56 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.58 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 662 HIS 0.001 0.000 HIS B 703 PHE 0.009 0.001 PHE B 471 TYR 0.016 0.001 TYR B 555 ARG 0.002 0.000 ARG A 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00020 ( 2) link_NAG-ASN : angle 1.83952 ( 6) link_BETA1-4 : bond 0.00494 ( 2) link_BETA1-4 : angle 1.07524 ( 6) hydrogen bonds : bond 0.03768 ( 496) hydrogen bonds : angle 3.73385 ( 1452) covalent geometry : bond 0.00265 ( 8778) covalent geometry : angle 0.49371 (11942) Misc. bond : bond 0.00032 ( 8) ********************** 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: 4 poor density : 45 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.9423 (mtm) cc_final: 0.8993 (mtm) REVERT: A 853 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8982 (t) REVERT: B 853 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.8998 (t) outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.2921 time to fit residues: 21.6163 Evaluate side-chains 49 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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: 0.8980 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.2823 r_free = 0.2823 target = 0.054772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.044711 restraints weight = 26908.839| |-----------------------------------------------------------------------------| r_work (start): 0.2540 rms_B_bonded: 2.99 r_work: 0.2400 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2906 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= 0.137 Angle : 0.511 7.167 11954 Z= 0.252 Chirality : 0.038 0.117 1436 Planarity : 0.004 0.046 1396 Dihedral : 7.814 58.787 1830 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.45 % Allowed : 9.06 % 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: 2.38 (0.27), residues: 1012 helix: 2.53 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -0.58 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 A 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00029 ( 2) link_NAG-ASN : angle 1.79147 ( 6) link_BETA1-4 : bond 0.00451 ( 2) link_BETA1-4 : angle 1.05533 ( 6) hydrogen bonds : bond 0.04032 ( 496) hydrogen bonds : angle 3.77893 ( 1452) covalent geometry : bond 0.00326 ( 8778) covalent geometry : angle 0.50949 (11942) Misc. bond : bond 0.00047 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3780.24 seconds wall clock time: 68 minutes 12.45 seconds (4092.45 seconds total)