Starting phenix.real_space_refine on Wed Sep 17 09:13:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mlk_48374/09_2025/9mlk_48374.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mlk_48374/09_2025/9mlk_48374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mlk_48374/09_2025/9mlk_48374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mlk_48374/09_2025/9mlk_48374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mlk_48374/09_2025/9mlk_48374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mlk_48374/09_2025/9mlk_48374.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 4604 2.51 5 N 1246 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7335 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 942 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 804 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "I" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 948 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "M" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "J" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 948 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "N" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 804 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "A" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 668 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 703 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 703 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 1.57, per 1000 atoms: 0.21 Number of scatterers: 7335 At special positions: 0 Unit cell: (116.16, 118.8, 89.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1446 8.00 N 1246 7.00 C 4604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 87 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 87 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 297.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 17 sheets defined 27.2% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.566A pdb=" N THR H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.901A pdb=" N LYS I 65 " --> pdb=" O PRO I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.682A pdb=" N THR I 91 " --> pdb=" O THR I 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 82 removed outlier: 3.628A pdb=" N ALA M 82 " --> pdb=" O ALA M 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 66 No H-bonds generated for 'chain 'J' and resid 64 through 66' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.644A pdb=" N ASP N 81 " --> pdb=" O GLU N 78 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA N 82 " --> pdb=" O ALA N 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 78 through 82' Processing helix chain 'A' and resid 503 through 546 removed outlier: 3.566A pdb=" N HIS A 545 " --> pdb=" O MET A 541 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 removed outlier: 3.715A pdb=" N VAL A 575 " --> pdb=" O HIS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 603 removed outlier: 3.601A pdb=" N SER A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 547 removed outlier: 3.554A pdb=" N SER C 517 " --> pdb=" O ASN C 513 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 518 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 581 Processing helix chain 'C' and resid 587 through 602 removed outlier: 3.804A pdb=" N SER C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 602 " --> pdb=" O PHE C 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 548 removed outlier: 3.825A pdb=" N GLN B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 589 through 602 removed outlier: 3.507A pdb=" N PHE B 598 " --> pdb=" O LYS B 594 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.327A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.670A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.427A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TYR L 48 " --> pdb=" O MET L 32 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N MET L 32 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.692A pdb=" N PHE I 79 " --> pdb=" O CYS I 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.402A pdb=" N TRP I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR I 51 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.257A pdb=" N CYS I 96 " --> pdb=" O TRP I 109 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TRP I 109 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG I 98 " --> pdb=" O ALA I 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.908A pdb=" N VAL M 19 " --> pdb=" O ILE M 74 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER M 69 " --> pdb=" O SER M 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 52 through 53 removed outlier: 6.543A pdb=" N TRP M 34 " --> pdb=" O TRP M 46 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR M 48 " --> pdb=" O MET M 32 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET M 32 " --> pdb=" O TYR M 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR M 96 " --> pdb=" O GLN M 89 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 52 through 53 removed outlier: 6.543A pdb=" N TRP M 34 " --> pdb=" O TRP M 46 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR M 48 " --> pdb=" O MET M 32 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET M 32 " --> pdb=" O TYR M 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.574A pdb=" N PHE J 79 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.385A pdb=" N TRP J 35 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR J 51 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP J 37 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.669A pdb=" N TYR J 108 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.622A pdb=" N THR N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 52 through 53 removed outlier: 6.699A pdb=" N TRP N 34 " --> pdb=" O TRP N 46 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR N 48 " --> pdb=" O MET N 32 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET N 32 " --> pdb=" O TYR N 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR N 84 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR N 96 " --> pdb=" O GLN N 89 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 52 through 53 removed outlier: 6.699A pdb=" N TRP N 34 " --> pdb=" O TRP N 46 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR N 48 " --> pdb=" O MET N 32 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET N 32 " --> pdb=" O TYR N 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR N 84 " --> pdb=" O GLN N 37 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1065 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: 0.99 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2340 1.34 - 1.46: 1479 1.46 - 1.57: 3620 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 7505 Sorted by residual: bond pdb=" CB TRP N 46 " pdb=" CG TRP N 46 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.01e+00 bond pdb=" C ASN H 84 " pdb=" N PRO H 85 " ideal model delta sigma weight residual 1.333 1.349 -0.016 1.20e-02 6.94e+03 1.73e+00 bond pdb=" C ASN J 84 " pdb=" N PRO J 85 " ideal model delta sigma weight residual 1.333 1.346 -0.013 1.20e-02 6.94e+03 1.24e+00 bond pdb=" C VAL I 12 " pdb=" N LYS I 13 " ideal model delta sigma weight residual 1.331 1.300 0.031 2.83e-02 1.25e+03 1.16e+00 bond pdb=" CG TRP N 46 " pdb=" CD2 TRP N 46 " ideal model delta sigma weight residual 1.433 1.418 0.015 1.80e-02 3.09e+03 6.77e-01 ... (remaining 7500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 10028 1.76 - 3.51: 130 3.51 - 5.27: 15 5.27 - 7.03: 5 7.03 - 8.78: 1 Bond angle restraints: 10179 Sorted by residual: angle pdb=" C LEU N 49 " pdb=" N THR N 50 " pdb=" CA THR N 50 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C LEU M 49 " pdb=" N THR M 50 " pdb=" CA THR M 50 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 angle pdb=" C LEU L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.86e+00 angle pdb=" CA LEU B 588 " pdb=" CB LEU B 588 " pdb=" CG LEU B 588 " ideal model delta sigma weight residual 116.30 125.08 -8.78 3.50e+00 8.16e-02 6.30e+00 angle pdb=" N GLY J 43 " pdb=" CA GLY J 43 " pdb=" C GLY J 43 " ideal model delta sigma weight residual 115.66 111.71 3.95 1.63e+00 3.76e-01 5.88e+00 ... (remaining 10174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4105 17.98 - 35.97: 302 35.97 - 53.95: 45 53.95 - 71.94: 13 71.94 - 89.92: 9 Dihedral angle restraints: 4474 sinusoidal: 1762 harmonic: 2712 Sorted by residual: dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " pdb=" CB CYS J 96 " ideal model delta sinusoidal sigma weight residual 93.00 156.63 -63.63 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 152.90 -59.90 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " pdb=" CB CYS I 96 " ideal model delta sinusoidal sigma weight residual 93.00 151.98 -58.98 1 1.00e+01 1.00e-02 4.65e+01 ... (remaining 4471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 721 0.029 - 0.057: 262 0.057 - 0.086: 62 0.086 - 0.114: 47 0.114 - 0.143: 17 Chirality restraints: 1109 Sorted by residual: chirality pdb=" CA THR N 50 " pdb=" N THR N 50 " pdb=" C THR N 50 " pdb=" CB THR N 50 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA THR M 50 " pdb=" N THR M 50 " pdb=" C THR M 50 " pdb=" CB THR M 50 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA LEU C 586 " pdb=" N LEU C 586 " pdb=" C LEU C 586 " pdb=" CB LEU C 586 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1106 not shown) Planarity restraints: 1284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP N 46 " 0.025 2.00e-02 2.50e+03 1.57e-02 6.18e+00 pdb=" CG TRP N 46 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP N 46 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP N 46 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP N 46 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP N 46 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP N 46 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 46 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 46 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP N 46 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU N 49 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C LEU N 49 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU N 49 " -0.010 2.00e-02 2.50e+03 pdb=" N THR N 50 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU M 49 " -0.005 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C LEU M 49 " 0.019 2.00e-02 2.50e+03 pdb=" O LEU M 49 " -0.007 2.00e-02 2.50e+03 pdb=" N THR M 50 " -0.006 2.00e-02 2.50e+03 ... (remaining 1281 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1055 2.76 - 3.29: 6845 3.29 - 3.83: 11922 3.83 - 4.36: 14286 4.36 - 4.90: 25593 Nonbonded interactions: 59701 Sorted by model distance: nonbonded pdb=" NE2 HIS C 545 " pdb=" OE1 GLU C 569 " model vdw 2.221 3.120 nonbonded pdb=" OG SER L 76 " pdb=" OE2 GLU L 78 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR L 70 " pdb=" OE1 GLU C 583 " model vdw 2.260 3.040 nonbonded pdb=" OG SER N 14 " pdb=" OE2 GLU N 17 " model vdw 2.262 3.040 nonbonded pdb=" O TRP N 46 " pdb=" N ALA N 54 " model vdw 2.306 3.120 ... (remaining 59696 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 502 through 546 or resid 569 through 603)) selection = (chain 'C' and (resid 502 through 546 or resid 569 through 603)) } ncs_group { reference = chain 'H' selection = (chain 'I' and resid 1 through 120) selection = (chain 'J' and resid 1 through 120) } ncs_group { reference = chain 'L' selection = (chain 'M' and resid 1 through 106) selection = chain 'N' } 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: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.450 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:7.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 : 0.003 0.054 7511 Z= 0.122 Angle : 0.537 8.784 10191 Z= 0.285 Chirality : 0.039 0.143 1109 Planarity : 0.004 0.032 1284 Dihedral : 12.972 89.919 2706 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.29), residues: 905 helix: 2.83 (0.34), residues: 211 sheet: -0.33 (0.30), residues: 326 loop : -0.13 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 530 TYR 0.009 0.001 TYR M 48 PHE 0.015 0.001 PHE L 61 TRP 0.041 0.001 TRP N 46 HIS 0.003 0.001 HIS A 571 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7505) covalent geometry : angle 0.53648 (10179) SS BOND : bond 0.00193 ( 6) SS BOND : angle 0.61138 ( 12) hydrogen bonds : bond 0.25689 ( 370) hydrogen bonds : angle 8.69594 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 96 THR cc_start: 0.9304 (m) cc_final: 0.8857 (p) REVERT: I 3 GLN cc_start: 0.7883 (tt0) cc_final: 0.7266 (mt0) REVERT: I 45 GLU cc_start: 0.8547 (pm20) cc_final: 0.8270 (pm20) REVERT: I 65 LYS cc_start: 0.8513 (mmmm) cc_final: 0.8231 (mmtt) REVERT: M 74 ILE cc_start: 0.8502 (mt) cc_final: 0.8115 (mt) REVERT: M 102 LYS cc_start: 0.8112 (tttt) cc_final: 0.7776 (tttp) REVERT: J 82 GLN cc_start: 0.8413 (mt0) cc_final: 0.8192 (tm-30) REVERT: N 78 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7701 (mm-30) REVERT: A 515 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8729 (tp-100) REVERT: A 519 ASP cc_start: 0.9130 (m-30) cc_final: 0.8840 (m-30) REVERT: C 592 LYS cc_start: 0.8940 (tptp) cc_final: 0.8724 (tppt) REVERT: B 508 SER cc_start: 0.8787 (t) cc_final: 0.8332 (p) REVERT: B 515 GLN cc_start: 0.9202 (tp-100) cc_final: 0.8979 (tm-30) REVERT: B 527 ASN cc_start: 0.8980 (m110) cc_final: 0.8670 (m-40) REVERT: B 542 SER cc_start: 0.9330 (t) cc_final: 0.8868 (m) REVERT: B 569 GLU cc_start: 0.7940 (pm20) cc_final: 0.7442 (pm20) REVERT: B 591 SER cc_start: 0.9190 (p) cc_final: 0.8472 (m) REVERT: B 595 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8664 (mm-30) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.6485 time to fit residues: 167.9095 Evaluate side-chains 192 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN M 37 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN A 527 ASN B 527 ASN B 545 HIS B 585 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.089121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.075567 restraints weight = 17433.242| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.78 r_work: 0.3064 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7511 Z= 0.172 Angle : 0.617 10.630 10191 Z= 0.326 Chirality : 0.041 0.141 1109 Planarity : 0.004 0.044 1284 Dihedral : 4.119 19.331 1002 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.59 % Allowed : 18.22 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.30), residues: 905 helix: 3.95 (0.33), residues: 211 sheet: -0.20 (0.30), residues: 327 loop : -0.09 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 539 TYR 0.020 0.001 TYR H 51 PHE 0.016 0.002 PHE H 79 TRP 0.021 0.001 TRP N 46 HIS 0.004 0.001 HIS C 545 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7505) covalent geometry : angle 0.61600 (10179) SS BOND : bond 0.00442 ( 6) SS BOND : angle 1.09279 ( 12) hydrogen bonds : bond 0.05872 ( 370) hydrogen bonds : angle 5.31037 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.7318 (tt0) cc_final: 0.6923 (tm-30) REVERT: I 45 GLU cc_start: 0.8479 (pm20) cc_final: 0.7938 (mp0) REVERT: I 65 LYS cc_start: 0.8563 (mmmm) cc_final: 0.8149 (mmtt) REVERT: M 17 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5647 (mp0) REVERT: M 74 ILE cc_start: 0.8271 (mt) cc_final: 0.8011 (mt) REVERT: M 106 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7426 (mttt) REVERT: J 82 GLN cc_start: 0.8435 (mt0) cc_final: 0.8122 (tm-30) REVERT: N 77 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.6083 (ttt) REVERT: N 78 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7736 (mm-30) REVERT: A 515 GLN cc_start: 0.8726 (tp-100) cc_final: 0.8343 (mm-40) REVERT: A 519 ASP cc_start: 0.8901 (m-30) cc_final: 0.8375 (m-30) REVERT: A 542 SER cc_start: 0.9602 (m) cc_final: 0.9343 (p) REVERT: A 592 LYS cc_start: 0.8997 (tptp) cc_final: 0.8744 (tptm) REVERT: C 528 ASP cc_start: 0.9266 (m-30) cc_final: 0.9000 (m-30) REVERT: C 592 LYS cc_start: 0.8882 (tptp) cc_final: 0.8592 (tppt) REVERT: B 508 SER cc_start: 0.8776 (t) cc_final: 0.8320 (p) REVERT: B 527 ASN cc_start: 0.8676 (m-40) cc_final: 0.8327 (m110) REVERT: B 569 GLU cc_start: 0.8305 (pm20) cc_final: 0.7525 (pm20) REVERT: B 583 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7323 (tm-30) REVERT: B 595 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8520 (mm-30) REVERT: B 599 GLU cc_start: 0.8452 (pm20) cc_final: 0.8206 (pm20) outliers start: 13 outliers final: 4 residues processed: 218 average time/residue: 0.6496 time to fit residues: 148.0316 Evaluate side-chains 194 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 188 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 77 MET Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 599 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN M 37 GLN N 6 GLN A 515 GLN A 527 ASN A 596 GLN ** C 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.086970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.073278 restraints weight = 17504.365| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.80 r_work: 0.3016 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7511 Z= 0.243 Angle : 0.640 8.563 10191 Z= 0.337 Chirality : 0.043 0.186 1109 Planarity : 0.004 0.033 1284 Dihedral : 4.320 18.373 1002 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.69 % Allowed : 21.27 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.30), residues: 905 helix: 3.97 (0.33), residues: 211 sheet: -0.18 (0.30), residues: 331 loop : -0.19 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 539 TYR 0.024 0.002 TYR J 51 PHE 0.017 0.002 PHE I 79 TRP 0.023 0.002 TRP N 46 HIS 0.002 0.001 HIS C 545 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 7505) covalent geometry : angle 0.63851 (10179) SS BOND : bond 0.00645 ( 6) SS BOND : angle 1.27963 ( 12) hydrogen bonds : bond 0.05501 ( 370) hydrogen bonds : angle 5.22109 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 11 MET cc_start: 0.8085 (ttp) cc_final: 0.7837 (ptm) REVERT: L 32 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.7625 (tpp) REVERT: I 3 GLN cc_start: 0.7379 (tt0) cc_final: 0.6951 (tm-30) REVERT: I 45 GLU cc_start: 0.8537 (pm20) cc_final: 0.7972 (mp0) REVERT: I 65 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8141 (mmtt) REVERT: M 17 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: M 74 ILE cc_start: 0.8284 (mt) cc_final: 0.8048 (mt) REVERT: M 102 LYS cc_start: 0.8158 (tttt) cc_final: 0.7838 (tttp) REVERT: M 106 LYS cc_start: 0.7934 (mtpp) cc_final: 0.7450 (mttt) REVERT: J 82 GLN cc_start: 0.8538 (mt0) cc_final: 0.8236 (tm130) REVERT: N 36 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: N 77 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.6184 (ttt) REVERT: N 78 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7701 (mm-30) REVERT: N 89 GLN cc_start: 0.9238 (pp30) cc_final: 0.8996 (pp30) REVERT: A 519 ASP cc_start: 0.8888 (m-30) cc_final: 0.8402 (m-30) REVERT: A 542 SER cc_start: 0.9543 (m) cc_final: 0.9333 (p) REVERT: A 592 LYS cc_start: 0.9109 (tptp) cc_final: 0.8883 (tptp) REVERT: C 592 LYS cc_start: 0.8904 (tptp) cc_final: 0.8620 (tppt) REVERT: B 505 GLN cc_start: 0.8587 (mp10) cc_final: 0.8247 (pm20) REVERT: B 506 LYS cc_start: 0.9065 (mppt) cc_final: 0.8583 (mptt) REVERT: B 508 SER cc_start: 0.8772 (t) cc_final: 0.8289 (p) REVERT: B 515 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8449 (mm-40) REVERT: B 527 ASN cc_start: 0.8735 (m-40) cc_final: 0.8361 (m110) REVERT: B 569 GLU cc_start: 0.8378 (pm20) cc_final: 0.7489 (pm20) REVERT: B 583 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7269 (tm-30) REVERT: B 595 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8664 (mm-30) REVERT: B 599 GLU cc_start: 0.8518 (pm20) cc_final: 0.8278 (mp0) outliers start: 22 outliers final: 7 residues processed: 209 average time/residue: 0.6444 time to fit residues: 140.8858 Evaluate side-chains 200 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 77 MET Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain C residue 517 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN M 37 GLN A 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.088213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.074510 restraints weight = 17587.341| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.81 r_work: 0.3035 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7511 Z= 0.165 Angle : 0.605 11.550 10191 Z= 0.313 Chirality : 0.040 0.140 1109 Planarity : 0.004 0.034 1284 Dihedral : 4.129 16.676 1002 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.57 % Allowed : 24.21 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.30), residues: 905 helix: 4.12 (0.33), residues: 211 sheet: -0.13 (0.30), residues: 329 loop : -0.14 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 539 TYR 0.014 0.001 TYR L 48 PHE 0.016 0.002 PHE H 79 TRP 0.012 0.001 TRP N 46 HIS 0.003 0.001 HIS C 545 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7505) covalent geometry : angle 0.60404 (10179) SS BOND : bond 0.00438 ( 6) SS BOND : angle 1.00102 ( 12) hydrogen bonds : bond 0.04767 ( 370) hydrogen bonds : angle 4.91518 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 11 MET cc_start: 0.8058 (ttp) cc_final: 0.7766 (ptm) REVERT: L 32 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.7450 (tpp) REVERT: I 3 GLN cc_start: 0.7328 (tt0) cc_final: 0.6912 (tm-30) REVERT: I 45 GLU cc_start: 0.8503 (pm20) cc_final: 0.7907 (mp0) REVERT: I 65 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8143 (mmtt) REVERT: M 17 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6247 (mp0) REVERT: M 74 ILE cc_start: 0.8261 (mt) cc_final: 0.8041 (mt) REVERT: M 106 LYS cc_start: 0.7986 (mtpp) cc_final: 0.7471 (mttt) REVERT: J 82 GLN cc_start: 0.8535 (mt0) cc_final: 0.8216 (tm130) REVERT: N 17 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7244 (mt-10) REVERT: N 36 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: N 77 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.6114 (ttt) REVERT: N 78 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7638 (mm-30) REVERT: A 519 ASP cc_start: 0.8882 (m-30) cc_final: 0.8466 (m-30) REVERT: C 541 MET cc_start: 0.8788 (tmm) cc_final: 0.8527 (tpt) REVERT: C 545 HIS cc_start: 0.8492 (m-70) cc_final: 0.8043 (m-70) REVERT: C 592 LYS cc_start: 0.8851 (tptp) cc_final: 0.8590 (tppt) REVERT: B 505 GLN cc_start: 0.8537 (mp10) cc_final: 0.8158 (pm20) REVERT: B 508 SER cc_start: 0.8831 (t) cc_final: 0.8361 (p) REVERT: B 515 GLN cc_start: 0.8709 (tp-100) cc_final: 0.8410 (mm-40) REVERT: B 569 GLU cc_start: 0.8390 (pm20) cc_final: 0.7537 (pm20) REVERT: B 583 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7243 (tm-30) REVERT: B 595 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8530 (mm-30) REVERT: B 598 PHE cc_start: 0.8542 (t80) cc_final: 0.8336 (t80) outliers start: 21 outliers final: 8 residues processed: 210 average time/residue: 0.6293 time to fit residues: 138.4996 Evaluate side-chains 203 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 77 MET Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 568 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN A 527 ASN B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.073421 restraints weight = 17587.576| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.84 r_work: 0.3029 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7511 Z= 0.197 Angle : 0.626 10.076 10191 Z= 0.325 Chirality : 0.041 0.141 1109 Planarity : 0.004 0.037 1284 Dihedral : 4.167 17.315 1002 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.81 % Allowed : 25.18 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.30), residues: 905 helix: 3.99 (0.33), residues: 211 sheet: -0.04 (0.30), residues: 325 loop : -0.21 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 530 TYR 0.027 0.001 TYR J 51 PHE 0.017 0.002 PHE C 598 TRP 0.014 0.001 TRP N 46 HIS 0.003 0.001 HIS C 545 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 7505) covalent geometry : angle 0.62491 (10179) SS BOND : bond 0.00534 ( 6) SS BOND : angle 1.16166 ( 12) hydrogen bonds : bond 0.04802 ( 370) hydrogen bonds : angle 4.93887 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 TYR cc_start: 0.8918 (p90) cc_final: 0.8675 (p90) REVERT: L 11 MET cc_start: 0.8153 (ttp) cc_final: 0.7807 (ptm) REVERT: L 32 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.7500 (tpp) REVERT: I 3 GLN cc_start: 0.7338 (tt0) cc_final: 0.6932 (tm-30) REVERT: I 45 GLU cc_start: 0.8503 (pm20) cc_final: 0.7960 (mp0) REVERT: I 65 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8161 (mmtt) REVERT: M 17 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6402 (mp0) REVERT: M 74 ILE cc_start: 0.8229 (mt) cc_final: 0.7991 (mt) REVERT: J 82 GLN cc_start: 0.8576 (mt0) cc_final: 0.8224 (tm-30) REVERT: N 1 ASP cc_start: 0.7497 (m-30) cc_final: 0.7234 (t0) REVERT: N 17 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7068 (mt-10) REVERT: N 36 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: N 77 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.6157 (ttt) REVERT: N 78 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 519 ASP cc_start: 0.8888 (m-30) cc_final: 0.8442 (m-30) REVERT: C 545 HIS cc_start: 0.8478 (m-70) cc_final: 0.8221 (m-70) REVERT: C 592 LYS cc_start: 0.8882 (tptp) cc_final: 0.8630 (tppt) REVERT: C 599 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8183 (mm-30) REVERT: B 505 GLN cc_start: 0.8545 (mp10) cc_final: 0.8260 (pm20) REVERT: B 506 LYS cc_start: 0.9090 (mppt) cc_final: 0.8524 (mptt) REVERT: B 508 SER cc_start: 0.8858 (t) cc_final: 0.8389 (p) REVERT: B 515 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8406 (mm-40) REVERT: B 569 GLU cc_start: 0.8391 (pm20) cc_final: 0.7527 (pm20) REVERT: B 583 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7233 (tm-30) REVERT: B 586 LEU cc_start: 0.8330 (tp) cc_final: 0.8105 (tp) REVERT: B 595 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8497 (mm-30) outliers start: 23 outliers final: 9 residues processed: 210 average time/residue: 0.6236 time to fit residues: 137.1245 Evaluate side-chains 199 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 77 MET Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 568 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 77 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN M 37 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.088026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.074507 restraints weight = 17343.294| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.77 r_work: 0.3040 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7511 Z= 0.165 Angle : 0.625 10.674 10191 Z= 0.322 Chirality : 0.041 0.144 1109 Planarity : 0.004 0.035 1284 Dihedral : 4.077 16.293 1002 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.81 % Allowed : 26.77 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.30), residues: 905 helix: 4.00 (0.33), residues: 211 sheet: 0.02 (0.30), residues: 325 loop : -0.19 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 539 TYR 0.014 0.001 TYR L 48 PHE 0.016 0.002 PHE H 79 TRP 0.010 0.001 TRP N 46 HIS 0.002 0.000 HIS C 545 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7505) covalent geometry : angle 0.62454 (10179) SS BOND : bond 0.00427 ( 6) SS BOND : angle 1.08930 ( 12) hydrogen bonds : bond 0.04501 ( 370) hydrogen bonds : angle 4.79860 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: H 16 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6807 (mp10) REVERT: H 51 TYR cc_start: 0.8924 (p90) cc_final: 0.8664 (OUTLIER) REVERT: L 11 MET cc_start: 0.8084 (ttp) cc_final: 0.7718 (ptm) REVERT: L 32 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.7415 (tpp) REVERT: I 3 GLN cc_start: 0.7328 (tt0) cc_final: 0.6914 (tm-30) REVERT: I 45 GLU cc_start: 0.8481 (pm20) cc_final: 0.7949 (mp0) REVERT: I 65 LYS cc_start: 0.8580 (mmmm) cc_final: 0.8159 (mmtt) REVERT: M 17 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: M 74 ILE cc_start: 0.8242 (mt) cc_final: 0.7961 (mt) REVERT: M 81 ASP cc_start: 0.8384 (m-30) cc_final: 0.7827 (m-30) REVERT: M 106 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7306 (mttt) REVERT: J 82 GLN cc_start: 0.8594 (mt0) cc_final: 0.8225 (tm-30) REVERT: N 1 ASP cc_start: 0.7506 (m-30) cc_final: 0.7240 (t0) REVERT: N 17 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7041 (mt-10) REVERT: N 36 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: N 77 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.6204 (ttt) REVERT: N 78 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 503 ASP cc_start: 0.8761 (p0) cc_final: 0.8557 (p0) REVERT: A 519 ASP cc_start: 0.8872 (m-30) cc_final: 0.8470 (m-30) REVERT: A 592 LYS cc_start: 0.8912 (tptp) cc_final: 0.8664 (tptp) REVERT: C 592 LYS cc_start: 0.8881 (tptp) cc_final: 0.8622 (tppt) REVERT: C 599 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8153 (mm-30) REVERT: B 505 GLN cc_start: 0.8529 (mp10) cc_final: 0.8291 (pm20) REVERT: B 506 LYS cc_start: 0.9106 (mppt) cc_final: 0.8540 (mptt) REVERT: B 508 SER cc_start: 0.8873 (t) cc_final: 0.8380 (p) REVERT: B 515 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8418 (mm-40) REVERT: B 569 GLU cc_start: 0.8354 (pm20) cc_final: 0.7512 (pm20) REVERT: B 583 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7162 (tm-30) REVERT: B 586 LEU cc_start: 0.8264 (tp) cc_final: 0.8002 (tp) REVERT: B 595 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8489 (mm-30) outliers start: 23 outliers final: 9 residues processed: 211 average time/residue: 0.6248 time to fit residues: 138.0981 Evaluate side-chains 209 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 77 MET Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain C residue 517 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN M 37 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS C 585 ASN B 527 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.085230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.071483 restraints weight = 17758.761| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.80 r_work: 0.2987 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 7511 Z= 0.332 Angle : 0.726 10.740 10191 Z= 0.377 Chirality : 0.045 0.156 1109 Planarity : 0.004 0.034 1284 Dihedral : 4.513 19.769 1002 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.81 % Allowed : 26.89 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.29), residues: 905 helix: 3.73 (0.33), residues: 211 sheet: -0.02 (0.30), residues: 319 loop : -0.46 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 539 TYR 0.026 0.002 TYR J 51 PHE 0.018 0.002 PHE I 79 TRP 0.023 0.002 TRP N 46 HIS 0.002 0.001 HIS C 571 Details of bonding type rmsd covalent geometry : bond 0.00783 ( 7505) covalent geometry : angle 0.72429 (10179) SS BOND : bond 0.00841 ( 6) SS BOND : angle 1.47928 ( 12) hydrogen bonds : bond 0.05326 ( 370) hydrogen bonds : angle 5.24558 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 51 TYR cc_start: 0.8925 (p90) cc_final: 0.8663 (p90) REVERT: L 32 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.7866 (tpp) REVERT: I 3 GLN cc_start: 0.7405 (tt0) cc_final: 0.6986 (tm-30) REVERT: I 45 GLU cc_start: 0.8543 (pm20) cc_final: 0.7962 (mp0) REVERT: I 65 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8164 (mmtt) REVERT: M 17 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6280 (mp0) REVERT: M 102 LYS cc_start: 0.8141 (tttt) cc_final: 0.7830 (tttp) REVERT: M 106 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7575 (mtmt) REVERT: J 82 GLN cc_start: 0.8696 (mt0) cc_final: 0.8286 (tm-30) REVERT: N 1 ASP cc_start: 0.7520 (m-30) cc_final: 0.7277 (t0) REVERT: N 36 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: N 77 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.6612 (ttt) REVERT: N 89 GLN cc_start: 0.9224 (pp30) cc_final: 0.8900 (pp30) REVERT: A 519 ASP cc_start: 0.8949 (m-30) cc_final: 0.8495 (m-30) REVERT: C 592 LYS cc_start: 0.8920 (tptp) cc_final: 0.8649 (tppt) REVERT: C 595 GLU cc_start: 0.8632 (tp30) cc_final: 0.7991 (tp30) REVERT: C 599 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8058 (mm-30) REVERT: B 505 GLN cc_start: 0.8634 (mp10) cc_final: 0.8328 (pm20) REVERT: B 506 LYS cc_start: 0.9124 (mppt) cc_final: 0.8557 (mptt) REVERT: B 508 SER cc_start: 0.8850 (t) cc_final: 0.8342 (p) REVERT: B 515 GLN cc_start: 0.8710 (tp-100) cc_final: 0.8483 (mm-40) REVERT: B 569 GLU cc_start: 0.8400 (pm20) cc_final: 0.7504 (pm20) REVERT: B 583 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7289 (tm-30) REVERT: B 585 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.6965 (p0) REVERT: B 589 ASP cc_start: 0.8782 (p0) cc_final: 0.8480 (p0) REVERT: B 595 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8530 (mm-30) outliers start: 23 outliers final: 10 residues processed: 205 average time/residue: 0.6369 time to fit residues: 136.4221 Evaluate side-chains 208 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 77 MET Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 585 ASN Chi-restraints excluded: chain B residue 585 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN M 37 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 HIS C 570 HIS B 527 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.088359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.074757 restraints weight = 17383.185| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.81 r_work: 0.3051 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7511 Z= 0.147 Angle : 0.647 11.353 10191 Z= 0.334 Chirality : 0.041 0.143 1109 Planarity : 0.004 0.040 1284 Dihedral : 4.156 16.226 1002 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.57 % Allowed : 27.87 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.29), residues: 905 helix: 3.74 (0.33), residues: 211 sheet: 0.01 (0.30), residues: 325 loop : -0.27 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 539 TYR 0.012 0.001 TYR L 48 PHE 0.015 0.001 PHE H 79 TRP 0.011 0.001 TRP J 35 HIS 0.002 0.001 HIS C 545 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7505) covalent geometry : angle 0.64690 (10179) SS BOND : bond 0.00325 ( 6) SS BOND : angle 0.93955 ( 12) hydrogen bonds : bond 0.04468 ( 370) hydrogen bonds : angle 4.84226 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6727 (mp10) REVERT: H 51 TYR cc_start: 0.8895 (p90) cc_final: 0.8636 (OUTLIER) REVERT: H 60 TYR cc_start: 0.9384 (m-80) cc_final: 0.9157 (m-80) REVERT: H 65 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7854 (ttmt) REVERT: L 11 MET cc_start: 0.8061 (ttp) cc_final: 0.7777 (ptm) REVERT: L 32 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.7526 (tpp) REVERT: I 3 GLN cc_start: 0.7300 (tt0) cc_final: 0.6861 (tm-30) REVERT: I 45 GLU cc_start: 0.8498 (pm20) cc_final: 0.7961 (mp0) REVERT: I 65 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8129 (mmtt) REVERT: M 17 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: M 81 ASP cc_start: 0.8399 (m-30) cc_final: 0.7892 (m-30) REVERT: M 106 LYS cc_start: 0.7978 (mtpp) cc_final: 0.7479 (mtmt) REVERT: J 82 GLN cc_start: 0.8655 (mt0) cc_final: 0.8235 (tm-30) REVERT: N 1 ASP cc_start: 0.7479 (m-30) cc_final: 0.7268 (t0) REVERT: N 17 GLU cc_start: 0.7271 (mt-10) cc_final: 0.7004 (mt-10) REVERT: N 36 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: N 77 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.6074 (ttt) REVERT: N 78 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7626 (mm-30) REVERT: A 519 ASP cc_start: 0.8881 (m-30) cc_final: 0.8445 (m-30) REVERT: A 592 LYS cc_start: 0.8922 (tptp) cc_final: 0.8655 (tptp) REVERT: C 541 MET cc_start: 0.8873 (tmm) cc_final: 0.8551 (tpp) REVERT: C 592 LYS cc_start: 0.8835 (tptp) cc_final: 0.8589 (tppt) REVERT: C 599 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8180 (mm-30) REVERT: B 505 GLN cc_start: 0.8552 (mp10) cc_final: 0.8328 (pm20) REVERT: B 506 LYS cc_start: 0.9100 (mppt) cc_final: 0.8547 (mptt) REVERT: B 508 SER cc_start: 0.8856 (t) cc_final: 0.8395 (p) REVERT: B 569 GLU cc_start: 0.8331 (pm20) cc_final: 0.7503 (pm20) REVERT: B 583 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7208 (tm-30) REVERT: B 585 ASN cc_start: 0.7576 (OUTLIER) cc_final: 0.6852 (p0) REVERT: B 586 LEU cc_start: 0.8228 (tp) cc_final: 0.7932 (tp) REVERT: B 589 ASP cc_start: 0.8780 (p0) cc_final: 0.8470 (p0) REVERT: B 595 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8553 (mm-30) outliers start: 21 outliers final: 8 residues processed: 213 average time/residue: 0.6066 time to fit residues: 135.2442 Evaluate side-chains 208 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 77 MET Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain B residue 585 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN A 515 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS B 527 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.088085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.074557 restraints weight = 17243.685| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.77 r_work: 0.3043 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7511 Z= 0.164 Angle : 0.654 11.374 10191 Z= 0.337 Chirality : 0.041 0.141 1109 Planarity : 0.004 0.036 1284 Dihedral : 4.101 16.077 1002 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.20 % Allowed : 28.73 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.29), residues: 905 helix: 3.78 (0.33), residues: 211 sheet: 0.08 (0.30), residues: 317 loop : -0.24 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 539 TYR 0.028 0.001 TYR J 51 PHE 0.024 0.002 PHE C 598 TRP 0.009 0.001 TRP H 35 HIS 0.004 0.001 HIS C 570 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7505) covalent geometry : angle 0.65387 (10179) SS BOND : bond 0.00426 ( 6) SS BOND : angle 1.04981 ( 12) hydrogen bonds : bond 0.04494 ( 370) hydrogen bonds : angle 4.86441 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6742 (mp10) REVERT: H 51 TYR cc_start: 0.8906 (p90) cc_final: 0.8657 (OUTLIER) REVERT: H 60 TYR cc_start: 0.9394 (m-80) cc_final: 0.9193 (m-80) REVERT: H 65 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7807 (ttmt) REVERT: L 11 MET cc_start: 0.8005 (ttp) cc_final: 0.7723 (ptm) REVERT: L 32 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.7483 (tpp) REVERT: I 3 GLN cc_start: 0.7328 (tt0) cc_final: 0.6890 (tm-30) REVERT: I 45 GLU cc_start: 0.8509 (pm20) cc_final: 0.7969 (mp0) REVERT: I 65 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8149 (mmtt) REVERT: M 17 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.5817 (mp0) REVERT: M 81 ASP cc_start: 0.8412 (m-30) cc_final: 0.7859 (m-30) REVERT: M 106 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7479 (mttt) REVERT: J 82 GLN cc_start: 0.8603 (mt0) cc_final: 0.8212 (tm-30) REVERT: N 17 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7027 (mt-10) REVERT: N 36 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: N 77 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.6074 (ttt) REVERT: N 78 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7558 (mm-30) REVERT: A 519 ASP cc_start: 0.8977 (m-30) cc_final: 0.8587 (m-30) REVERT: C 541 MET cc_start: 0.8868 (tmm) cc_final: 0.8557 (tpp) REVERT: C 592 LYS cc_start: 0.8867 (tptp) cc_final: 0.8621 (tppt) REVERT: B 505 GLN cc_start: 0.8525 (mp10) cc_final: 0.8301 (pm20) REVERT: B 506 LYS cc_start: 0.9101 (mppt) cc_final: 0.8618 (mptt) REVERT: B 508 SER cc_start: 0.8857 (t) cc_final: 0.8370 (p) REVERT: B 546 ARG cc_start: 0.9165 (mtp180) cc_final: 0.8928 (ttm170) REVERT: B 569 GLU cc_start: 0.8330 (pm20) cc_final: 0.7523 (pm20) REVERT: B 583 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: B 585 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.6731 (p0) REVERT: B 586 LEU cc_start: 0.8257 (tp) cc_final: 0.7941 (tp) REVERT: B 589 ASP cc_start: 0.8786 (p0) cc_final: 0.8510 (p0) REVERT: B 595 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8578 (mm-30) outliers start: 18 outliers final: 8 residues processed: 204 average time/residue: 0.6080 time to fit residues: 130.0445 Evaluate side-chains 208 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 77 MET Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 585 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN A 545 HIS ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.088491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.074830 restraints weight = 17374.879| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.82 r_work: 0.3047 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.004 0.045 7511 Z= 0.157 Angle : 0.683 12.129 10191 Z= 0.351 Chirality : 0.041 0.148 1109 Planarity : 0.004 0.037 1284 Dihedral : 4.106 18.833 1002 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.83 % Allowed : 29.22 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.30), residues: 905 helix: 3.67 (0.34), residues: 211 sheet: 0.05 (0.30), residues: 323 loop : -0.11 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 539 TYR 0.028 0.001 TYR J 51 PHE 0.015 0.001 PHE H 79 TRP 0.010 0.001 TRP J 35 HIS 0.003 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7505) covalent geometry : angle 0.68286 (10179) SS BOND : bond 0.00378 ( 6) SS BOND : angle 1.00025 ( 12) hydrogen bonds : bond 0.04390 ( 370) hydrogen bonds : angle 4.80599 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 16 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6732 (mp10) REVERT: H 51 TYR cc_start: 0.8896 (p90) cc_final: 0.8655 (OUTLIER) REVERT: H 60 TYR cc_start: 0.9390 (m-80) cc_final: 0.9179 (m-80) REVERT: H 65 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7793 (ttmt) REVERT: L 11 MET cc_start: 0.7979 (ttp) cc_final: 0.7698 (ptm) REVERT: L 17 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7475 (pt0) REVERT: L 32 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.7503 (tpp) REVERT: I 3 GLN cc_start: 0.7332 (tt0) cc_final: 0.6884 (tm-30) REVERT: I 45 GLU cc_start: 0.8500 (pm20) cc_final: 0.7958 (mp0) REVERT: I 65 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8124 (mmtt) REVERT: M 17 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.5810 (mp0) REVERT: M 81 ASP cc_start: 0.8450 (m-30) cc_final: 0.7894 (m-30) REVERT: M 106 LYS cc_start: 0.7965 (mtpp) cc_final: 0.7488 (mttt) REVERT: J 82 GLN cc_start: 0.8567 (mt0) cc_final: 0.8202 (tm-30) REVERT: N 17 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7034 (mt-10) REVERT: N 36 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: N 77 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.6015 (ttt) REVERT: N 78 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7599 (mm-30) REVERT: A 519 ASP cc_start: 0.8981 (m-30) cc_final: 0.8608 (m-30) REVERT: C 541 MET cc_start: 0.8887 (tmm) cc_final: 0.8571 (tpp) REVERT: C 592 LYS cc_start: 0.8839 (tptp) cc_final: 0.8524 (tppt) REVERT: C 596 GLN cc_start: 0.8482 (mt0) cc_final: 0.8205 (mt0) REVERT: B 505 GLN cc_start: 0.8524 (mp10) cc_final: 0.8302 (pm20) REVERT: B 506 LYS cc_start: 0.9099 (mppt) cc_final: 0.8614 (mptt) REVERT: B 508 SER cc_start: 0.8829 (t) cc_final: 0.8392 (p) REVERT: B 569 GLU cc_start: 0.8293 (pm20) cc_final: 0.7515 (pm20) REVERT: B 583 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6721 (tm-30) REVERT: B 585 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.6986 (p0) REVERT: B 589 ASP cc_start: 0.8863 (p0) cc_final: 0.8635 (p0) REVERT: B 595 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8575 (mm-30) outliers start: 15 outliers final: 7 residues processed: 204 average time/residue: 0.6290 time to fit residues: 134.4499 Evaluate side-chains 205 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 77 MET Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 585 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN A 545 HIS ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS B 527 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.086692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.072819 restraints weight = 17637.516| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.83 r_work: 0.3016 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 7511 Z= 0.239 Angle : 0.727 10.944 10191 Z= 0.377 Chirality : 0.043 0.143 1109 Planarity : 0.004 0.034 1284 Dihedral : 4.335 21.352 1002 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.20 % Allowed : 28.97 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.30), residues: 905 helix: 3.63 (0.34), residues: 209 sheet: 0.04 (0.31), residues: 318 loop : -0.33 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 539 TYR 0.023 0.001 TYR I 51 PHE 0.033 0.002 PHE C 598 TRP 0.015 0.001 TRP N 46 HIS 0.003 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 7505) covalent geometry : angle 0.72579 (10179) SS BOND : bond 0.00642 ( 6) SS BOND : angle 1.28147 ( 12) hydrogen bonds : bond 0.04882 ( 370) hydrogen bonds : angle 5.08279 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3062.62 seconds wall clock time: 53 minutes 0.31 seconds (3180.31 seconds total)