Starting phenix.real_space_refine on Fri Jun 13 18:46:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8svf_40789/06_2025/8svf_40789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8svf_40789/06_2025/8svf_40789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8svf_40789/06_2025/8svf_40789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8svf_40789/06_2025/8svf_40789.map" model { file = "/net/cci-nas-00/data/ceres_data/8svf_40789/06_2025/8svf_40789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8svf_40789/06_2025/8svf_40789.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 295 5.49 5 S 25 5.16 5 C 8678 2.51 5 N 2835 2.21 5 O 3421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15254 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 753 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 669 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3138 Classifications: {'DNA': 152} Link IDs: {'rna3p': 151} Chain: "J" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2909 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2122 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 100 Chain: "L" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 738 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "M" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 438 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 9.29, per 1000 atoms: 0.61 Number of scatterers: 15254 At special positions: 0 Unit cell: (121.181, 142.256, 116.966, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 295 15.00 O 3421 8.00 N 2835 7.00 C 8678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.31 Conformation dependent library (CDL) restraints added in 1.4 seconds 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2230 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 64.8% alpha, 5.9% beta 142 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 6.26 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.569A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.500A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.523A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.893A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.531A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.593A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.945A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.502A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.572A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.708A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.514A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.610A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.612A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 11 through 23 Processing helix chain 'K' and resid 36 through 40 removed outlier: 3.730A pdb=" N GLN K 40 " --> pdb=" O SER K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 78 Processing helix chain 'K' and resid 90 through 102 removed outlier: 3.697A pdb=" N ASN K 102 " --> pdb=" O SER K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 120 removed outlier: 3.867A pdb=" N LEU K 112 " --> pdb=" O LEU K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 133 Processing helix chain 'K' and resid 134 through 143 Processing helix chain 'K' and resid 202 through 218 removed outlier: 3.759A pdb=" N ALA K 206 " --> pdb=" O TRP K 202 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL K 209 " --> pdb=" O LYS K 205 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR K 218 " --> pdb=" O ILE K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 244 Processing helix chain 'K' and resid 647 through 668 Processing helix chain 'K' and resid 671 through 686 Processing helix chain 'K' and resid 687 through 696 Processing helix chain 'L' and resid 257 through 262 Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 269 through 276 removed outlier: 3.683A pdb=" N LEU L 276 " --> pdb=" O THR L 272 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 286 Processing helix chain 'L' and resid 310 through 327 Processing helix chain 'L' and resid 330 through 345 Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.787A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.582A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.286A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.046A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.819A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.464A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 27 through 31 removed outlier: 4.558A pdb=" N GLY K 194 " --> pdb=" O LEU K 180 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU K 182 " --> pdb=" O ASP K 192 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP K 192 " --> pdb=" O GLU K 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 293 through 295 Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 15 removed outlier: 6.404A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU M 71 " --> pdb=" O LYS M 6 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU M 43 " --> pdb=" O LEU M 50 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 366 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 6.80 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3041 1.33 - 1.45: 4844 1.45 - 1.57: 7608 1.57 - 1.69: 588 1.69 - 1.81: 43 Bond restraints: 16124 Sorted by residual: bond pdb=" N ASN K 695 " pdb=" CA ASN K 695 " ideal model delta sigma weight residual 1.455 1.497 -0.042 1.25e-02 6.40e+03 1.11e+01 bond pdb=" N ILE K 696 " pdb=" CA ILE K 696 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.37e+00 bond pdb=" N VAL K 692 " pdb=" CA VAL K 692 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 7.95e+00 bond pdb=" N MET K 687 " pdb=" CA MET K 687 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.33e-02 5.65e+03 6.36e+00 bond pdb=" C ASN K 695 " pdb=" O ASN K 695 " ideal model delta sigma weight residual 1.236 1.269 -0.033 1.33e-02 5.65e+03 6.13e+00 ... (remaining 16119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 21712 1.03 - 2.06: 1051 2.06 - 3.09: 275 3.09 - 4.13: 23 4.13 - 5.16: 8 Bond angle restraints: 23069 Sorted by residual: angle pdb=" C SER K 697 " pdb=" N VAL K 698 " pdb=" CA VAL K 698 " ideal model delta sigma weight residual 123.10 118.69 4.41 1.29e+00 6.01e-01 1.17e+01 angle pdb=" CA GLN K 694 " pdb=" C GLN K 694 " pdb=" O GLN K 694 " ideal model delta sigma weight residual 120.70 117.44 3.26 1.03e+00 9.43e-01 1.00e+01 angle pdb=" CA ALA K 219 " pdb=" C ALA K 219 " pdb=" O ALA K 219 " ideal model delta sigma weight residual 122.45 118.43 4.02 1.30e+00 5.92e-01 9.56e+00 angle pdb=" N GLU K 693 " pdb=" CA GLU K 693 " pdb=" C GLU K 693 " ideal model delta sigma weight residual 111.71 108.27 3.44 1.15e+00 7.56e-01 8.97e+00 angle pdb=" N GLY K 197 " pdb=" CA GLY K 197 " pdb=" C GLY K 197 " ideal model delta sigma weight residual 112.77 108.98 3.79 1.28e+00 6.10e-01 8.78e+00 ... (remaining 23064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 7549 35.09 - 70.19: 1333 70.19 - 105.28: 15 105.28 - 140.37: 0 140.37 - 175.47: 2 Dihedral angle restraints: 8899 sinusoidal: 5460 harmonic: 3439 Sorted by residual: dihedral pdb=" C4' DT I 153 " pdb=" C3' DT I 153 " pdb=" O3' DT I 153 " pdb=" P DC I 154 " ideal model delta sinusoidal sigma weight residual 220.00 44.53 175.47 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG I 119 " pdb=" C3' DG I 119 " pdb=" O3' DG I 119 " pdb=" P DG I 120 " ideal model delta sinusoidal sigma weight residual 220.00 69.83 150.17 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CA TRP K 196 " pdb=" C TRP K 196 " pdb=" N GLY K 197 " pdb=" CA GLY K 197 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 8896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2131 0.041 - 0.081: 421 0.081 - 0.122: 83 0.122 - 0.162: 6 0.162 - 0.203: 2 Chirality restraints: 2643 Sorted by residual: chirality pdb=" CA ILE K 696 " pdb=" N ILE K 696 " pdb=" C ILE K 696 " pdb=" CB ILE K 696 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA LEU K 691 " pdb=" N LEU K 691 " pdb=" C LEU K 691 " pdb=" CB LEU K 691 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA VAL K 692 " pdb=" N VAL K 692 " pdb=" C VAL K 692 " pdb=" CB VAL K 692 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 2640 not shown) Planarity restraints: 1916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 146 " 0.025 2.00e-02 2.50e+03 1.09e-02 3.25e+00 pdb=" N9 DA I 146 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 146 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 146 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 146 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 146 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 146 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 146 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 146 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 146 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 146 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 135 " 0.023 2.00e-02 2.50e+03 9.97e-03 2.74e+00 pdb=" N9 DA I 135 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DA I 135 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 135 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA I 135 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 135 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 135 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 135 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 135 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 135 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 135 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 254 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO L 255 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO L 255 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 255 " -0.023 5.00e-02 4.00e+02 ... (remaining 1913 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1967 2.76 - 3.29: 13781 3.29 - 3.83: 28727 3.83 - 4.36: 32449 4.36 - 4.90: 49531 Nonbonded interactions: 126455 Sorted by model distance: nonbonded pdb=" O PHE K 122 " pdb=" NZ LYS K 127 " model vdw 2.220 3.120 nonbonded pdb=" NE2 HIS K 169 " pdb=" OD1 ASP K 184 " model vdw 2.228 3.120 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.292 3.040 nonbonded pdb=" O ILE M 36 " pdb=" NE2 GLN M 41 " model vdw 2.315 3.120 nonbonded pdb=" O MET K 115 " pdb=" OG1 THR K 119 " model vdw 2.327 3.040 ... (remaining 126450 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' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 110)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 110)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 41.170 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 0.042 16124 Z= 0.177 Angle : 0.531 5.156 23069 Z= 0.336 Chirality : 0.034 0.203 2643 Planarity : 0.003 0.041 1916 Dihedral : 24.962 175.468 6669 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.28 % Allowed : 3.43 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.25), residues: 1159 helix: 2.90 (0.19), residues: 721 sheet: 1.29 (0.78), residues: 48 loop : -0.07 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 52 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE K 50 TYR 0.007 0.001 TYR G 57 ARG 0.002 0.000 ARG K 60 Details of bonding type rmsd hydrogen bonds : bond 0.10976 ( 935) hydrogen bonds : angle 3.82475 ( 2385) covalent geometry : bond 0.00344 (16124) covalent geometry : angle 0.53097 (23069) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 264 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8368 (mmmt) cc_final: 0.8156 (tttp) REVERT: A 107 THR cc_start: 0.9408 (m) cc_final: 0.9019 (p) REVERT: B 53 GLU cc_start: 0.8379 (tp30) cc_final: 0.8068 (tp30) REVERT: B 63 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7642 (mt-10) REVERT: C 75 LYS cc_start: 0.9181 (mttm) cc_final: 0.8874 (mtpp) REVERT: C 90 ASP cc_start: 0.8826 (t0) cc_final: 0.8469 (t0) REVERT: E 90 MET cc_start: 0.9002 (mmp) cc_final: 0.8800 (mmm) REVERT: F 25 ASN cc_start: 0.8405 (m-40) cc_final: 0.8200 (m-40) REVERT: G 90 ASP cc_start: 0.8322 (t0) cc_final: 0.7136 (t0) REVERT: G 100 VAL cc_start: 0.9682 (t) cc_final: 0.9422 (p) REVERT: K 53 ILE cc_start: 0.4429 (OUTLIER) cc_final: 0.4087 (pp) REVERT: K 231 MET cc_start: 0.7609 (mtm) cc_final: 0.7028 (mtt) REVERT: L 262 THR cc_start: 0.9066 (m) cc_final: 0.8637 (t) REVERT: L 312 PHE cc_start: 0.9043 (m-80) cc_final: 0.8406 (m-80) REVERT: L 321 ARG cc_start: 0.9020 (ttp-110) cc_final: 0.8819 (ptm160) REVERT: L 334 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8381 (mm-40) REVERT: L 336 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.8260 (tmt170) outliers start: 12 outliers final: 4 residues processed: 271 average time/residue: 0.3776 time to fit residues: 139.1328 Evaluate side-chains 192 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 59 ARG Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN D 81 ASN D 92 GLN F 93 GLN G 24 GLN G 31 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.092307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.058450 restraints weight = 55834.961| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.26 r_work: 0.2975 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16124 Z= 0.187 Angle : 0.552 12.164 23069 Z= 0.325 Chirality : 0.036 0.172 2643 Planarity : 0.004 0.043 1916 Dihedral : 28.956 174.427 4528 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.14 % Allowed : 9.64 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.24), residues: 1159 helix: 2.75 (0.19), residues: 738 sheet: 0.98 (0.75), residues: 48 loop : -0.10 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 52 HIS 0.006 0.001 HIS K 169 PHE 0.020 0.001 PHE L 252 TYR 0.011 0.001 TYR K 173 ARG 0.006 0.000 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 935) hydrogen bonds : angle 3.02951 ( 2385) covalent geometry : bond 0.00416 (16124) covalent geometry : angle 0.55178 (23069) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7549 (mtp85) cc_final: 0.7067 (mpt180) REVERT: A 79 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8141 (tttp) REVERT: A 107 THR cc_start: 0.9433 (m) cc_final: 0.9034 (p) REVERT: B 63 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8317 (mt-10) REVERT: C 56 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8877 (tm-30) REVERT: C 64 GLU cc_start: 0.9153 (tt0) cc_final: 0.8867 (tm-30) REVERT: C 90 ASP cc_start: 0.9044 (t0) cc_final: 0.8679 (t0) REVERT: F 25 ASN cc_start: 0.8863 (m-40) cc_final: 0.8658 (m-40) REVERT: F 63 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8230 (tm-30) REVERT: F 74 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8761 (mt-10) REVERT: G 90 ASP cc_start: 0.8224 (t0) cc_final: 0.7586 (t0) REVERT: G 92 GLU cc_start: 0.8522 (pm20) cc_final: 0.8313 (pm20) REVERT: G 100 VAL cc_start: 0.9752 (t) cc_final: 0.9489 (p) REVERT: H 68 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8935 (tp30) REVERT: H 102 GLU cc_start: 0.8351 (mp0) cc_final: 0.7953 (tt0) REVERT: K 231 MET cc_start: 0.8095 (mtm) cc_final: 0.7332 (mtt) REVERT: K 695 ASN cc_start: 0.8552 (t0) cc_final: 0.8232 (t0) REVERT: L 251 ASP cc_start: 0.6424 (t0) cc_final: 0.5880 (t0) REVERT: L 286 PHE cc_start: 0.8845 (m-10) cc_final: 0.8461 (t80) REVERT: L 321 ARG cc_start: 0.9042 (ttp-110) cc_final: 0.8786 (ptm160) REVERT: L 334 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8426 (mm-40) REVERT: L 336 ARG cc_start: 0.8522 (ttm-80) cc_final: 0.8160 (tmt170) outliers start: 20 outliers final: 13 residues processed: 204 average time/residue: 0.3057 time to fit residues: 88.6680 Evaluate side-chains 192 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 704 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 31 HIS E 68 GLN K 169 HIS ** K 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.093623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.060125 restraints weight = 55684.731| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.28 r_work: 0.3011 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16124 Z= 0.139 Angle : 0.511 8.586 23069 Z= 0.305 Chirality : 0.034 0.128 2643 Planarity : 0.004 0.047 1916 Dihedral : 28.855 175.720 4522 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.50 % Allowed : 11.24 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.24), residues: 1159 helix: 2.91 (0.19), residues: 736 sheet: 0.70 (0.73), residues: 48 loop : -0.07 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 52 HIS 0.010 0.001 HIS K 169 PHE 0.021 0.001 PHE K 170 TYR 0.021 0.001 TYR B 88 ARG 0.006 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 935) hydrogen bonds : angle 2.80761 ( 2385) covalent geometry : bond 0.00297 (16124) covalent geometry : angle 0.51084 (23069) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7487 (mtp85) cc_final: 0.7003 (mpt180) REVERT: A 79 LYS cc_start: 0.8370 (mmmt) cc_final: 0.8094 (tttp) REVERT: A 107 THR cc_start: 0.9432 (m) cc_final: 0.9038 (p) REVERT: B 63 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8347 (mt-10) REVERT: B 88 TYR cc_start: 0.9019 (m-10) cc_final: 0.8749 (m-10) REVERT: C 56 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8826 (tm-30) REVERT: C 64 GLU cc_start: 0.9194 (tt0) cc_final: 0.8876 (tm-30) REVERT: C 90 ASP cc_start: 0.8993 (t0) cc_final: 0.8601 (t0) REVERT: F 25 ASN cc_start: 0.8856 (m-40) cc_final: 0.8613 (m-40) REVERT: F 63 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8152 (tm-30) REVERT: G 38 ASN cc_start: 0.9208 (m-40) cc_final: 0.8912 (p0) REVERT: G 90 ASP cc_start: 0.8157 (t0) cc_final: 0.7412 (t0) REVERT: G 92 GLU cc_start: 0.8457 (pm20) cc_final: 0.8086 (pm20) REVERT: G 100 VAL cc_start: 0.9743 (t) cc_final: 0.9479 (p) REVERT: H 68 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8934 (tp30) REVERT: K 231 MET cc_start: 0.7934 (mtm) cc_final: 0.7319 (mtt) REVERT: K 695 ASN cc_start: 0.8529 (t0) cc_final: 0.8225 (t0) REVERT: L 251 ASP cc_start: 0.6185 (t0) cc_final: 0.5944 (t0) REVERT: L 286 PHE cc_start: 0.8873 (m-10) cc_final: 0.8508 (t80) REVERT: L 321 ARG cc_start: 0.9001 (ttp-110) cc_final: 0.8786 (ptm160) REVERT: L 334 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8296 (mm-40) REVERT: L 336 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8159 (tmt170) outliers start: 14 outliers final: 11 residues processed: 203 average time/residue: 0.3189 time to fit residues: 92.5583 Evaluate side-chains 186 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 687 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 137 optimal weight: 30.0000 chunk 43 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 118 optimal weight: 30.0000 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN K 169 HIS L 274 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.092374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.059495 restraints weight = 55161.591| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.17 r_work: 0.2994 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16124 Z= 0.160 Angle : 0.519 7.871 23069 Z= 0.308 Chirality : 0.034 0.151 2643 Planarity : 0.004 0.044 1916 Dihedral : 28.909 175.825 4521 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.71 % Allowed : 12.74 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.25), residues: 1159 helix: 2.94 (0.19), residues: 738 sheet: 0.71 (0.74), residues: 48 loop : -0.03 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 52 HIS 0.012 0.001 HIS K 169 PHE 0.010 0.001 PHE K 50 TYR 0.012 0.001 TYR B 88 ARG 0.005 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 935) hydrogen bonds : angle 2.81357 ( 2385) covalent geometry : bond 0.00353 (16124) covalent geometry : angle 0.51856 (23069) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7456 (mtp85) cc_final: 0.6968 (mpt180) REVERT: A 79 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8139 (tttp) REVERT: A 107 THR cc_start: 0.9449 (m) cc_final: 0.9065 (p) REVERT: B 63 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8401 (mt-10) REVERT: C 56 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8862 (tm-30) REVERT: C 64 GLU cc_start: 0.9201 (tt0) cc_final: 0.8887 (tm-30) REVERT: C 90 ASP cc_start: 0.9026 (t0) cc_final: 0.8654 (t0) REVERT: F 25 ASN cc_start: 0.8724 (m-40) cc_final: 0.8480 (m-40) REVERT: F 63 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8218 (tm-30) REVERT: G 90 ASP cc_start: 0.8274 (t0) cc_final: 0.7660 (t0) REVERT: G 100 VAL cc_start: 0.9749 (t) cc_final: 0.9478 (p) REVERT: H 68 GLU cc_start: 0.9239 (tm-30) cc_final: 0.8931 (tp30) REVERT: K 226 ILE cc_start: 0.0341 (OUTLIER) cc_final: -0.0047 (tt) REVERT: K 231 MET cc_start: 0.7921 (mtm) cc_final: 0.7389 (mtt) REVERT: K 695 ASN cc_start: 0.8662 (t0) cc_final: 0.8308 (t0) REVERT: L 251 ASP cc_start: 0.6378 (t0) cc_final: 0.5781 (t0) REVERT: L 286 PHE cc_start: 0.8889 (m-10) cc_final: 0.8481 (t80) REVERT: L 334 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8380 (mm-40) REVERT: L 336 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.8211 (tmt170) outliers start: 16 outliers final: 11 residues processed: 189 average time/residue: 0.2916 time to fit residues: 79.0759 Evaluate side-chains 186 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 19 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN E 68 GLN K 169 HIS L 274 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.092936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.059586 restraints weight = 56225.793| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.23 r_work: 0.2998 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16124 Z= 0.147 Angle : 0.514 6.864 23069 Z= 0.305 Chirality : 0.034 0.144 2643 Planarity : 0.004 0.042 1916 Dihedral : 28.889 176.302 4521 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.71 % Allowed : 14.24 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.25), residues: 1159 helix: 2.98 (0.19), residues: 738 sheet: 0.66 (0.73), residues: 48 loop : -0.08 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 52 HIS 0.012 0.001 HIS K 169 PHE 0.017 0.001 PHE L 252 TYR 0.028 0.001 TYR B 88 ARG 0.005 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 935) hydrogen bonds : angle 2.76078 ( 2385) covalent geometry : bond 0.00320 (16124) covalent geometry : angle 0.51367 (23069) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8387 (mmmt) cc_final: 0.8146 (tttp) REVERT: A 107 THR cc_start: 0.9460 (m) cc_final: 0.9074 (p) REVERT: A 125 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8907 (mm-40) REVERT: B 63 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8394 (mt-10) REVERT: B 77 LYS cc_start: 0.9408 (mttp) cc_final: 0.9107 (mmtm) REVERT: B 88 TYR cc_start: 0.9001 (m-10) cc_final: 0.8639 (m-10) REVERT: B 92 ARG cc_start: 0.9328 (ttp80) cc_final: 0.9034 (ttp80) REVERT: C 56 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8845 (tm-30) REVERT: C 63 LEU cc_start: 0.9135 (mt) cc_final: 0.8883 (mt) REVERT: C 64 GLU cc_start: 0.9212 (tt0) cc_final: 0.8986 (tm-30) REVERT: C 90 ASP cc_start: 0.9031 (t0) cc_final: 0.8630 (t0) REVERT: C 92 GLU cc_start: 0.8405 (tp30) cc_final: 0.7820 (tp30) REVERT: D 80 TYR cc_start: 0.8190 (m-10) cc_final: 0.7676 (m-10) REVERT: F 25 ASN cc_start: 0.8682 (m-40) cc_final: 0.8144 (m110) REVERT: F 63 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8171 (tm-30) REVERT: G 90 ASP cc_start: 0.8306 (t0) cc_final: 0.7585 (t0) REVERT: G 92 GLU cc_start: 0.8602 (pm20) cc_final: 0.8195 (pm20) REVERT: G 100 VAL cc_start: 0.9745 (t) cc_final: 0.9474 (p) REVERT: H 68 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8946 (tp30) REVERT: K 226 ILE cc_start: 0.0099 (OUTLIER) cc_final: -0.0305 (tt) REVERT: K 231 MET cc_start: 0.7971 (mtm) cc_final: 0.7454 (mtt) REVERT: K 695 ASN cc_start: 0.8582 (t0) cc_final: 0.8117 (m110) REVERT: L 251 ASP cc_start: 0.6531 (t0) cc_final: 0.6114 (t0) REVERT: L 334 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8445 (mm-40) REVERT: L 336 ARG cc_start: 0.8519 (ttm-80) cc_final: 0.8191 (tmt170) outliers start: 16 outliers final: 11 residues processed: 184 average time/residue: 0.2959 time to fit residues: 79.9884 Evaluate side-chains 181 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 687 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 0.0670 chunk 102 optimal weight: 30.0000 chunk 53 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN E 68 GLN K 169 HIS L 274 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.092680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.059295 restraints weight = 56111.996| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.24 r_work: 0.2989 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16124 Z= 0.153 Angle : 0.522 7.833 23069 Z= 0.307 Chirality : 0.034 0.157 2643 Planarity : 0.004 0.040 1916 Dihedral : 28.906 176.640 4521 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.25 % Allowed : 13.81 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.25), residues: 1159 helix: 3.04 (0.19), residues: 732 sheet: 0.66 (0.73), residues: 48 loop : -0.01 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 52 HIS 0.013 0.001 HIS K 169 PHE 0.012 0.001 PHE L 252 TYR 0.023 0.001 TYR B 88 ARG 0.005 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 935) hydrogen bonds : angle 2.73823 ( 2385) covalent geometry : bond 0.00337 (16124) covalent geometry : angle 0.52211 (23069) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9458 (m) cc_final: 0.9068 (p) REVERT: A 125 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8897 (mm-40) REVERT: B 63 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8401 (mt-10) REVERT: B 77 LYS cc_start: 0.9420 (mttp) cc_final: 0.9202 (mmtm) REVERT: B 84 MET cc_start: 0.8841 (mmm) cc_final: 0.8521 (mmm) REVERT: B 88 TYR cc_start: 0.9028 (m-10) cc_final: 0.8394 (m-10) REVERT: C 56 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8882 (tm-30) REVERT: C 64 GLU cc_start: 0.9190 (tt0) cc_final: 0.8973 (tm-30) REVERT: C 90 ASP cc_start: 0.9088 (t0) cc_final: 0.8733 (t0) REVERT: D 80 TYR cc_start: 0.8215 (m-10) cc_final: 0.7817 (m-10) REVERT: F 25 ASN cc_start: 0.8647 (m-40) cc_final: 0.8117 (m110) REVERT: F 63 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8199 (tm-30) REVERT: G 90 ASP cc_start: 0.8276 (t0) cc_final: 0.7531 (t0) REVERT: G 100 VAL cc_start: 0.9746 (t) cc_final: 0.9471 (p) REVERT: H 68 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8924 (tp30) REVERT: K 226 ILE cc_start: 0.0509 (OUTLIER) cc_final: 0.0101 (tt) REVERT: K 231 MET cc_start: 0.8033 (mtm) cc_final: 0.7440 (mtt) REVERT: L 251 ASP cc_start: 0.6631 (t0) cc_final: 0.6191 (t0) REVERT: L 334 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8430 (mm-40) REVERT: L 336 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8207 (tmt170) outliers start: 21 outliers final: 13 residues processed: 185 average time/residue: 0.3498 time to fit residues: 93.6016 Evaluate side-chains 182 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 687 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 46 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 116 optimal weight: 30.0000 chunk 59 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 89 ASN K 169 HIS L 274 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.089466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.055488 restraints weight = 56598.430| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.26 r_work: 0.2887 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 16124 Z= 0.305 Angle : 0.644 6.035 23069 Z= 0.371 Chirality : 0.040 0.194 2643 Planarity : 0.005 0.037 1916 Dihedral : 29.420 176.144 4521 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.25 % Allowed : 14.35 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.25), residues: 1159 helix: 2.70 (0.19), residues: 732 sheet: 0.53 (0.72), residues: 48 loop : -0.35 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 52 HIS 0.015 0.002 HIS K 169 PHE 0.013 0.002 PHE G 25 TYR 0.031 0.002 TYR B 88 ARG 0.005 0.001 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.05708 ( 935) hydrogen bonds : angle 3.29946 ( 2385) covalent geometry : bond 0.00693 (16124) covalent geometry : angle 0.64431 (23069) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8831 (mm-40) REVERT: A 131 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8535 (mtt90) REVERT: B 63 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8477 (mt-10) REVERT: B 88 TYR cc_start: 0.9074 (m-10) cc_final: 0.8838 (m-10) REVERT: C 56 GLU cc_start: 0.9288 (tm-30) cc_final: 0.9018 (tm-30) REVERT: C 64 GLU cc_start: 0.9242 (tt0) cc_final: 0.8980 (tm-30) REVERT: C 75 LYS cc_start: 0.9328 (mttm) cc_final: 0.9055 (mtpp) REVERT: C 90 ASP cc_start: 0.9141 (t0) cc_final: 0.8841 (t0) REVERT: F 25 ASN cc_start: 0.8739 (m-40) cc_final: 0.8429 (m-40) REVERT: F 63 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8412 (tm-30) REVERT: G 90 ASP cc_start: 0.8506 (t0) cc_final: 0.7814 (t0) REVERT: G 92 GLU cc_start: 0.8778 (pm20) cc_final: 0.8490 (pm20) REVERT: G 100 VAL cc_start: 0.9767 (t) cc_final: 0.9463 (p) REVERT: H 68 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8903 (tp30) REVERT: K 54 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7174 (pm20) REVERT: K 226 ILE cc_start: 0.0837 (OUTLIER) cc_final: 0.0458 (tt) REVERT: K 231 MET cc_start: 0.8003 (mtm) cc_final: 0.7766 (mtt) REVERT: L 334 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8413 (mm-40) REVERT: L 336 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8248 (tmt170) outliers start: 21 outliers final: 13 residues processed: 171 average time/residue: 0.3165 time to fit residues: 79.5532 Evaluate side-chains 172 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 687 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 89 ASN K 169 HIS L 274 HIS M 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.090070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.056368 restraints weight = 56143.882| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.22 r_work: 0.2921 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16124 Z= 0.212 Angle : 0.574 6.220 23069 Z= 0.335 Chirality : 0.036 0.186 2643 Planarity : 0.004 0.040 1916 Dihedral : 29.312 176.757 4521 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.03 % Allowed : 14.78 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.25), residues: 1159 helix: 2.89 (0.19), residues: 730 sheet: 0.43 (0.71), residues: 48 loop : -0.39 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 52 HIS 0.015 0.001 HIS K 169 PHE 0.011 0.001 PHE K 50 TYR 0.021 0.001 TYR B 88 ARG 0.006 0.000 ARG M 42 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 935) hydrogen bonds : angle 3.02887 ( 2385) covalent geometry : bond 0.00477 (16124) covalent geometry : angle 0.57414 (23069) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8872 (mm-40) REVERT: A 131 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8558 (mtt90) REVERT: B 63 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8490 (mt-10) REVERT: B 88 TYR cc_start: 0.9074 (m-10) cc_final: 0.8854 (m-10) REVERT: C 56 GLU cc_start: 0.9277 (tm-30) cc_final: 0.8989 (tm-30) REVERT: C 90 ASP cc_start: 0.9103 (t0) cc_final: 0.8795 (t0) REVERT: F 25 ASN cc_start: 0.8769 (m-40) cc_final: 0.8409 (m-40) REVERT: F 63 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8293 (tm-30) REVERT: G 90 ASP cc_start: 0.8396 (t0) cc_final: 0.7802 (t0) REVERT: G 92 GLU cc_start: 0.8580 (pm20) cc_final: 0.8333 (pm20) REVERT: G 100 VAL cc_start: 0.9768 (t) cc_final: 0.9472 (p) REVERT: H 68 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8889 (tp30) REVERT: K 54 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: K 226 ILE cc_start: 0.0777 (OUTLIER) cc_final: 0.0435 (tt) REVERT: K 231 MET cc_start: 0.8044 (mtm) cc_final: 0.7377 (mtt) REVERT: L 334 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8410 (mm-40) REVERT: L 336 ARG cc_start: 0.8606 (ttm-80) cc_final: 0.8251 (tmt170) outliers start: 19 outliers final: 12 residues processed: 174 average time/residue: 0.3004 time to fit residues: 76.1014 Evaluate side-chains 173 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 687 MET Chi-restraints excluded: chain K residue 704 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 52 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 169 HIS K 695 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.091095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.057620 restraints weight = 55824.628| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.19 r_work: 0.2962 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16124 Z= 0.159 Angle : 0.563 9.130 23069 Z= 0.327 Chirality : 0.035 0.178 2643 Planarity : 0.004 0.040 1916 Dihedral : 29.160 176.925 4521 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.82 % Allowed : 15.52 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.25), residues: 1159 helix: 2.94 (0.19), residues: 731 sheet: 0.59 (0.74), residues: 48 loop : -0.34 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 52 HIS 0.016 0.001 HIS K 169 PHE 0.010 0.001 PHE K 50 TYR 0.018 0.001 TYR B 88 ARG 0.006 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 935) hydrogen bonds : angle 2.86889 ( 2385) covalent geometry : bond 0.00353 (16124) covalent geometry : angle 0.56327 (23069) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8865 (mm-40) REVERT: B 63 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8435 (mt-10) REVERT: B 84 MET cc_start: 0.8863 (mmm) cc_final: 0.8566 (mmm) REVERT: B 88 TYR cc_start: 0.9073 (m-10) cc_final: 0.8534 (m-10) REVERT: C 56 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8897 (tm-30) REVERT: C 90 ASP cc_start: 0.9046 (t0) cc_final: 0.8725 (t0) REVERT: D 80 TYR cc_start: 0.8255 (m-10) cc_final: 0.7976 (m-10) REVERT: F 25 ASN cc_start: 0.8762 (m-40) cc_final: 0.8429 (m-40) REVERT: F 63 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8215 (tm-30) REVERT: G 90 ASP cc_start: 0.8334 (t0) cc_final: 0.7689 (t0) REVERT: G 92 GLU cc_start: 0.8538 (pm20) cc_final: 0.8089 (pm20) REVERT: G 100 VAL cc_start: 0.9763 (t) cc_final: 0.9469 (p) REVERT: H 68 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8901 (tp30) REVERT: K 54 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: K 226 ILE cc_start: 0.0760 (OUTLIER) cc_final: 0.0387 (tt) REVERT: K 231 MET cc_start: 0.8108 (mtm) cc_final: 0.7501 (mtt) REVERT: L 334 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8404 (mm-40) REVERT: L 336 ARG cc_start: 0.8591 (ttm-80) cc_final: 0.8215 (tmt170) REVERT: L 341 MET cc_start: 0.2907 (ptt) cc_final: 0.2692 (mtm) outliers start: 17 outliers final: 13 residues processed: 179 average time/residue: 0.2913 time to fit residues: 75.5474 Evaluate side-chains 181 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 687 MET Chi-restraints excluded: chain K residue 695 ASN Chi-restraints excluded: chain K residue 704 VAL Chi-restraints excluded: chain L residue 321 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 169 HIS K 695 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.090779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.057238 restraints weight = 56414.467| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.21 r_work: 0.2951 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16124 Z= 0.183 Angle : 0.572 8.574 23069 Z= 0.332 Chirality : 0.035 0.171 2643 Planarity : 0.004 0.056 1916 Dihedral : 29.164 177.115 4521 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.61 % Allowed : 15.63 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.25), residues: 1159 helix: 2.89 (0.19), residues: 732 sheet: 0.63 (0.74), residues: 48 loop : -0.39 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 52 HIS 0.016 0.001 HIS K 169 PHE 0.010 0.001 PHE K 50 TYR 0.018 0.001 TYR B 88 ARG 0.008 0.000 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 935) hydrogen bonds : angle 2.90876 ( 2385) covalent geometry : bond 0.00409 (16124) covalent geometry : angle 0.57175 (23069) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8816 (mm-40) REVERT: B 63 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8442 (mt-10) REVERT: B 84 MET cc_start: 0.8894 (mmm) cc_final: 0.8575 (mmm) REVERT: B 88 TYR cc_start: 0.9068 (m-10) cc_final: 0.8502 (m-10) REVERT: C 56 GLU cc_start: 0.9236 (tm-30) cc_final: 0.8938 (tm-30) REVERT: C 90 ASP cc_start: 0.9061 (t0) cc_final: 0.8761 (t0) REVERT: D 80 TYR cc_start: 0.8302 (m-10) cc_final: 0.7964 (m-10) REVERT: F 25 ASN cc_start: 0.8769 (m-40) cc_final: 0.8423 (m-40) REVERT: F 63 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8248 (tm-30) REVERT: G 90 ASP cc_start: 0.8275 (t0) cc_final: 0.7646 (t0) REVERT: G 100 VAL cc_start: 0.9768 (t) cc_final: 0.9467 (p) REVERT: H 68 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8902 (tp30) REVERT: K 54 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: K 226 ILE cc_start: 0.0771 (OUTLIER) cc_final: 0.0388 (tt) REVERT: K 231 MET cc_start: 0.8131 (mtm) cc_final: 0.7902 (mtt) REVERT: L 334 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8432 (mm-40) REVERT: L 336 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8210 (tmt170) outliers start: 15 outliers final: 11 residues processed: 169 average time/residue: 0.4026 time to fit residues: 100.8238 Evaluate side-chains 175 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 695 ASN Chi-restraints excluded: chain K residue 704 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 70 optimal weight: 4.9990 chunk 14 optimal weight: 0.0170 chunk 92 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 139 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 169 HIS K 695 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.091474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.058502 restraints weight = 55736.817| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.20 r_work: 0.2992 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16124 Z= 0.138 Angle : 0.555 8.695 23069 Z= 0.321 Chirality : 0.034 0.172 2643 Planarity : 0.004 0.059 1916 Dihedral : 29.017 177.379 4521 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.61 % Allowed : 15.95 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.25), residues: 1159 helix: 2.95 (0.19), residues: 731 sheet: 0.69 (0.74), residues: 48 loop : -0.34 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 52 HIS 0.016 0.001 HIS K 169 PHE 0.009 0.001 PHE K 50 TYR 0.012 0.001 TYR B 88 ARG 0.008 0.000 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 935) hydrogen bonds : angle 2.76732 ( 2385) covalent geometry : bond 0.00297 (16124) covalent geometry : angle 0.55464 (23069) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10698.13 seconds wall clock time: 188 minutes 25.99 seconds (11305.99 seconds total)