Starting phenix.real_space_refine on Sat Mar 16 17:25:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8svf_40789/03_2024/8svf_40789.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8svf_40789/03_2024/8svf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8svf_40789/03_2024/8svf_40789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8svf_40789/03_2024/8svf_40789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8svf_40789/03_2024/8svf_40789.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8svf_40789/03_2024/8svf_40789.pdb" } 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 Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.30, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 7.71 Conformation dependent library (CDL) restraints added in 1.7 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: 6.43 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: 10.47 Time building geometry restraints manager: 8.16 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: 99.02 - 106.02: 1814 106.02 - 113.03: 8764 113.03 - 120.03: 5939 120.03 - 127.03: 5855 127.03 - 134.03: 697 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 2.520 nonbonded pdb=" NE2 HIS K 169 " pdb=" OD1 ASP K 184 " model vdw 2.228 2.520 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.292 2.440 nonbonded pdb=" O ILE M 36 " pdb=" NE2 GLN M 41 " model vdw 2.315 2.520 nonbonded pdb=" O MET K 115 " pdb=" OG1 THR K 119 " model vdw 2.327 2.440 ... (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 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: 1.540 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: 6.590 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 52.010 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.010 ------------------------------------------------------------------------------- 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= 0.196 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 264 time to evaluate : 1.247 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: 0.3462 time to fit residues: 126.8284 Evaluate side-chains 192 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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: 8.9990 chunk 107 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 24 GLN G 31 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16124 Z= 0.319 Angle : 0.582 11.913 23069 Z= 0.341 Chirality : 0.038 0.364 2643 Planarity : 0.004 0.045 1916 Dihedral : 29.067 173.873 4528 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.68 % Allowed : 10.81 % Favored : 86.51 % 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: 2.60 (0.24), residues: 1159 helix: 2.66 (0.19), residues: 737 sheet: 1.01 (0.74), residues: 48 loop : -0.11 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 52 HIS 0.005 0.001 HIS F 75 PHE 0.014 0.001 PHE L 252 TYR 0.011 0.002 TYR K 173 ARG 0.006 0.001 ARG D 83 *********************** 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 206 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 1.375 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: 0.8413 (mmmt) cc_final: 0.8145 (tttm) REVERT: A 125 GLN cc_start: 0.8916 (mt0) cc_final: 0.8673 (mm-40) REVERT: B 63 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7729 (mt-10) REVERT: C 56 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8656 (tm-30) REVERT: C 90 ASP cc_start: 0.8908 (t0) cc_final: 0.8613 (t0) REVERT: D 79 HIS cc_start: 0.8647 (t-90) cc_final: 0.8401 (t-90) REVERT: G 90 ASP cc_start: 0.8171 (t0) cc_final: 0.7348 (t0) REVERT: G 92 GLU cc_start: 0.8165 (pm20) cc_final: 0.7875 (pm20) REVERT: G 100 VAL cc_start: 0.9705 (t) cc_final: 0.9419 (p) REVERT: H 68 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8536 (tp30) REVERT: K 231 MET cc_start: 0.8019 (mtm) cc_final: 0.7175 (mtt) REVERT: K 695 ASN cc_start: 0.8310 (t0) cc_final: 0.7928 (t0) REVERT: L 334 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8379 (mm-40) REVERT: L 336 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8282 (tmt170) outliers start: 25 outliers final: 18 residues processed: 198 average time/residue: 0.2955 time to fit residues: 83.2719 Evaluate side-chains 185 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 61 SER 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 E residue 112 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 184 ASP 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 71 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 87 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 30.0000 chunk 128 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 81 ASN ** K 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16124 Z= 0.237 Angle : 0.537 8.124 23069 Z= 0.318 Chirality : 0.035 0.135 2643 Planarity : 0.004 0.049 1916 Dihedral : 29.073 175.159 4522 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.14 % Allowed : 12.10 % Favored : 85.76 % 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: 2.68 (0.24), residues: 1159 helix: 2.79 (0.19), residues: 735 sheet: 0.90 (0.72), residues: 48 loop : -0.20 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 52 HIS 0.004 0.001 HIS F 75 PHE 0.013 0.001 PHE L 280 TYR 0.027 0.001 TYR B 88 ARG 0.005 0.000 ARG D 96 *********************** 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 196 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 176 time to evaluate : 1.142 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: 0.8381 (mmmt) cc_final: 0.8134 (tttp) REVERT: A 120 MET cc_start: 0.8430 (mtp) cc_final: 0.8134 (mtp) REVERT: B 63 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7853 (mt-10) REVERT: C 56 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8660 (tm-30) REVERT: C 90 ASP cc_start: 0.8916 (t0) cc_final: 0.8632 (t0) REVERT: F 63 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7628 (tm-30) REVERT: G 90 ASP cc_start: 0.8058 (t0) cc_final: 0.7463 (t0) REVERT: G 92 GLU cc_start: 0.8182 (pm20) cc_final: 0.7960 (pm20) REVERT: G 100 VAL cc_start: 0.9708 (t) cc_final: 0.9420 (p) REVERT: H 68 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8552 (tp30) REVERT: K 231 MET cc_start: 0.7828 (mtm) cc_final: 0.7138 (mtt) REVERT: K 695 ASN cc_start: 0.8361 (t0) cc_final: 0.7958 (t0) REVERT: L 333 MET cc_start: 0.7948 (mmp) cc_final: 0.7716 (mmp) REVERT: L 334 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8181 (mm-40) REVERT: L 336 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8265 (tmt170) outliers start: 20 outliers final: 16 residues processed: 189 average time/residue: 0.2820 time to fit residues: 77.0846 Evaluate side-chains 180 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 184 ASP 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 127 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 129 optimal weight: 8.9990 chunk 137 optimal weight: 40.0000 chunk 122 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2570 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= 0.311 Angle : 0.578 8.203 23069 Z= 0.338 Chirality : 0.037 0.186 2643 Planarity : 0.004 0.046 1916 Dihedral : 29.253 174.849 4522 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.75 % Allowed : 11.78 % Favored : 84.48 % 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: 2.60 (0.24), residues: 1159 helix: 2.75 (0.19), residues: 734 sheet: 0.69 (0.72), residues: 48 loop : -0.26 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 52 HIS 0.004 0.001 HIS K 193 PHE 0.012 0.001 PHE L 280 TYR 0.035 0.002 TYR B 88 ARG 0.005 0.000 ARG D 96 *********************** 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 203 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7868 (mt-10) REVERT: B 88 TYR cc_start: 0.8756 (m-10) cc_final: 0.8547 (m-10) REVERT: C 56 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8726 (tm-30) REVERT: C 90 ASP cc_start: 0.8965 (t0) cc_final: 0.8686 (t0) REVERT: F 63 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7630 (tm-30) REVERT: G 90 ASP cc_start: 0.8197 (t0) cc_final: 0.7510 (t0) REVERT: G 92 GLU cc_start: 0.8252 (pm20) cc_final: 0.7966 (pm20) REVERT: G 100 VAL cc_start: 0.9726 (t) cc_final: 0.9430 (p) REVERT: H 68 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8570 (tp30) REVERT: K 231 MET cc_start: 0.7797 (mtm) cc_final: 0.7506 (mtt) REVERT: K 695 ASN cc_start: 0.8221 (t0) cc_final: 0.7717 (t0) REVERT: L 336 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8259 (tmt170) outliers start: 35 outliers final: 24 residues processed: 191 average time/residue: 0.2761 time to fit residues: 76.1068 Evaluate side-chains 183 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 61 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 184 ASP 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 L residue 254 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16124 Z= 0.211 Angle : 0.534 6.923 23069 Z= 0.316 Chirality : 0.035 0.155 2643 Planarity : 0.004 0.042 1916 Dihedral : 29.139 175.531 4522 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.89 % Allowed : 13.70 % 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: 2.77 (0.25), residues: 1159 helix: 2.92 (0.19), residues: 735 sheet: 0.65 (0.73), residues: 48 loop : -0.28 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 52 HIS 0.014 0.001 HIS L 274 PHE 0.013 0.001 PHE L 252 TYR 0.019 0.001 TYR B 88 ARG 0.005 0.000 ARG D 96 *********************** 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 200 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8917 (mt0) cc_final: 0.8586 (mm-40) REVERT: B 63 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7817 (mt-10) REVERT: B 88 TYR cc_start: 0.8782 (m-10) cc_final: 0.8486 (m-10) REVERT: C 56 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8649 (tm-30) REVERT: C 64 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8439 (tm-30) REVERT: C 90 ASP cc_start: 0.8937 (t0) cc_final: 0.8658 (t0) REVERT: D 105 LYS cc_start: 0.8387 (tmmt) cc_final: 0.8147 (tmmt) REVERT: F 63 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7594 (tm-30) REVERT: G 90 ASP cc_start: 0.8159 (t0) cc_final: 0.7498 (t0) REVERT: G 92 GLU cc_start: 0.8230 (pm20) cc_final: 0.7954 (pm20) REVERT: G 100 VAL cc_start: 0.9722 (t) cc_final: 0.9430 (p) REVERT: H 68 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8549 (tp30) REVERT: K 54 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7251 (pm20) REVERT: K 231 MET cc_start: 0.7830 (mtm) cc_final: 0.7091 (mtt) REVERT: K 695 ASN cc_start: 0.8182 (t0) cc_final: 0.7725 (t0) REVERT: L 334 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8265 (mm-40) REVERT: L 336 ARG cc_start: 0.8548 (ttm-80) cc_final: 0.8266 (tmt170) outliers start: 27 outliers final: 20 residues processed: 189 average time/residue: 0.2703 time to fit residues: 74.7986 Evaluate side-chains 186 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 61 SER 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 44 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 184 ASP 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 L residue 254 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 137 optimal weight: 30.0000 chunk 114 optimal weight: 20.0000 chunk 63 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 132 optimal weight: 40.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS M 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16124 Z= 0.322 Angle : 0.584 6.580 23069 Z= 0.340 Chirality : 0.037 0.174 2643 Planarity : 0.004 0.041 1916 Dihedral : 29.297 175.451 4522 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.32 % Allowed : 14.67 % Favored : 82.01 % 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: 2.58 (0.25), residues: 1159 helix: 2.76 (0.19), residues: 736 sheet: 0.45 (0.71), residues: 48 loop : -0.30 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 52 HIS 0.018 0.001 HIS L 274 PHE 0.013 0.001 PHE L 252 TYR 0.021 0.002 TYR B 88 ARG 0.005 0.000 ARG D 96 *********************** 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 193 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7990 (mt-10) REVERT: B 88 TYR cc_start: 0.8833 (m-10) cc_final: 0.8633 (m-10) REVERT: C 56 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8718 (tm-30) REVERT: C 64 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8493 (tm-30) REVERT: C 90 ASP cc_start: 0.8955 (t0) cc_final: 0.8698 (t0) REVERT: D 105 LYS cc_start: 0.8424 (tmmt) cc_final: 0.8037 (tmmt) REVERT: F 63 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7637 (tm-30) REVERT: G 90 ASP cc_start: 0.8237 (t0) cc_final: 0.7519 (t0) REVERT: G 92 GLU cc_start: 0.8237 (pm20) cc_final: 0.7970 (pm20) REVERT: G 100 VAL cc_start: 0.9739 (t) cc_final: 0.9437 (p) REVERT: H 68 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8528 (tp30) REVERT: K 54 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: K 226 ILE cc_start: 0.0291 (OUTLIER) cc_final: -0.0107 (tt) REVERT: K 231 MET cc_start: 0.7891 (mtm) cc_final: 0.7165 (mtt) REVERT: K 695 ASN cc_start: 0.8175 (t0) cc_final: 0.7687 (t0) REVERT: L 334 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8303 (mm-40) REVERT: L 336 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.8250 (tmt170) outliers start: 31 outliers final: 24 residues processed: 181 average time/residue: 0.2792 time to fit residues: 73.7902 Evaluate side-chains 183 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU 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 61 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 184 ASP 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 L residue 254 THR Chi-restraints excluded: chain L residue 319 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** K 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16124 Z= 0.371 Angle : 0.613 6.677 23069 Z= 0.356 Chirality : 0.039 0.185 2643 Planarity : 0.004 0.041 1916 Dihedral : 29.485 175.699 4522 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.32 % Allowed : 14.35 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.25), residues: 1159 helix: 2.66 (0.19), residues: 735 sheet: 0.31 (0.73), residues: 48 loop : -0.50 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 52 HIS 0.006 0.001 HIS L 274 PHE 0.013 0.001 PHE L 252 TYR 0.021 0.002 TYR C 57 ARG 0.006 0.000 ARG E 116 *********************** 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 195 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7424 (mtp85) cc_final: 0.6932 (mpt180) REVERT: A 131 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8250 (mtt90) REVERT: B 88 TYR cc_start: 0.8839 (m-10) cc_final: 0.8616 (m-10) REVERT: C 56 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8715 (tm-30) REVERT: C 64 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8495 (tm-30) REVERT: C 75 LYS cc_start: 0.9258 (mttm) cc_final: 0.9023 (mtpp) REVERT: C 90 ASP cc_start: 0.8946 (t0) cc_final: 0.8695 (t0) REVERT: F 63 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7662 (tm-30) REVERT: G 90 ASP cc_start: 0.8297 (t0) cc_final: 0.7534 (t0) REVERT: G 92 GLU cc_start: 0.8273 (pm20) cc_final: 0.7962 (pm20) REVERT: G 100 VAL cc_start: 0.9763 (t) cc_final: 0.9462 (p) REVERT: H 68 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8487 (tp30) REVERT: K 54 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: K 226 ILE cc_start: 0.0172 (OUTLIER) cc_final: -0.0192 (tt) REVERT: K 231 MET cc_start: 0.7933 (mtm) cc_final: 0.7523 (mtt) REVERT: K 695 ASN cc_start: 0.8157 (t0) cc_final: 0.7659 (t0) REVERT: L 334 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8160 (mm-40) REVERT: L 336 ARG cc_start: 0.8586 (ttm-80) cc_final: 0.8285 (tmt170) REVERT: L 341 MET cc_start: 0.2654 (ptt) cc_final: 0.2380 (mtm) outliers start: 31 outliers final: 24 residues processed: 185 average time/residue: 0.2814 time to fit residues: 74.7178 Evaluate side-chains 187 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 170 PHE Chi-restraints excluded: chain K residue 184 ASP 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 L residue 254 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16124 Z= 0.191 Angle : 0.540 7.568 23069 Z= 0.318 Chirality : 0.035 0.157 2643 Planarity : 0.004 0.044 1916 Dihedral : 29.182 176.300 4522 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.46 % Allowed : 15.20 % Favored : 82.33 % 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: 2.68 (0.25), residues: 1159 helix: 2.89 (0.19), residues: 736 sheet: 0.32 (0.73), residues: 48 loop : -0.36 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 52 HIS 0.011 0.001 HIS L 274 PHE 0.010 0.001 PHE K 50 TYR 0.013 0.001 TYR C 57 ARG 0.006 0.000 ARG D 96 *********************** 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 201 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7353 (mtp85) cc_final: 0.6934 (mpt180) REVERT: A 131 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8146 (mtt90) REVERT: B 63 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7804 (mt-10) REVERT: B 77 LYS cc_start: 0.9261 (mttp) cc_final: 0.9016 (mptt) REVERT: C 56 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8630 (tm-30) REVERT: C 64 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8474 (tm-30) REVERT: C 90 ASP cc_start: 0.8897 (t0) cc_final: 0.8639 (t0) REVERT: F 63 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7616 (tm-30) REVERT: G 90 ASP cc_start: 0.8219 (t0) cc_final: 0.7518 (t0) REVERT: G 92 GLU cc_start: 0.8263 (pm20) cc_final: 0.7735 (pm20) REVERT: G 100 VAL cc_start: 0.9735 (t) cc_final: 0.9398 (p) REVERT: H 68 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8517 (tp30) REVERT: K 54 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: K 226 ILE cc_start: 0.0393 (OUTLIER) cc_final: 0.0064 (tt) REVERT: K 231 MET cc_start: 0.7997 (mtm) cc_final: 0.7660 (mtt) REVERT: K 695 ASN cc_start: 0.8059 (t0) cc_final: 0.7576 (t0) REVERT: L 334 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8186 (mm-40) REVERT: L 336 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8292 (tmt170) outliers start: 23 outliers final: 17 residues processed: 193 average time/residue: 0.3031 time to fit residues: 84.6296 Evaluate side-chains 189 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 61 SER 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 F residue 85 ASP Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 170 PHE Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain L residue 254 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 115 optimal weight: 30.0000 chunk 120 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS L 283 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3484 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= 0.216 Angle : 0.553 7.252 23069 Z= 0.324 Chirality : 0.035 0.191 2643 Planarity : 0.004 0.044 1916 Dihedral : 29.168 176.301 4520 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.68 % Allowed : 15.95 % Favored : 81.37 % 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: 2.66 (0.25), residues: 1159 helix: 2.87 (0.19), residues: 736 sheet: 0.38 (0.74), residues: 48 loop : -0.35 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 52 HIS 0.012 0.001 HIS L 274 PHE 0.012 0.001 PHE A 67 TYR 0.033 0.001 TYR B 88 ARG 0.006 0.000 ARG D 96 *********************** 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 198 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7347 (mtp85) cc_final: 0.6928 (mpt180) REVERT: A 131 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8142 (mtt90) REVERT: B 63 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7837 (mt-10) REVERT: B 84 MET cc_start: 0.8379 (mmm) cc_final: 0.8145 (mmm) REVERT: B 88 TYR cc_start: 0.8745 (m-10) cc_final: 0.7983 (m-10) REVERT: C 56 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8633 (tm-30) REVERT: C 64 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8477 (tm-30) REVERT: C 90 ASP cc_start: 0.8890 (t0) cc_final: 0.8638 (t0) REVERT: D 80 TYR cc_start: 0.7894 (m-10) cc_final: 0.7602 (m-10) REVERT: F 63 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7609 (tm-30) REVERT: G 90 ASP cc_start: 0.8156 (t0) cc_final: 0.7638 (t0) REVERT: G 100 VAL cc_start: 0.9737 (t) cc_final: 0.9409 (p) REVERT: H 68 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8483 (tp30) REVERT: K 54 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: K 226 ILE cc_start: 0.0398 (OUTLIER) cc_final: 0.0069 (tt) REVERT: K 231 MET cc_start: 0.8060 (mtm) cc_final: 0.7702 (mtt) REVERT: K 695 ASN cc_start: 0.8036 (t0) cc_final: 0.7560 (t0) REVERT: L 334 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8215 (mm-40) REVERT: L 336 ARG cc_start: 0.8465 (ttm-80) cc_final: 0.8111 (tmt170) outliers start: 25 outliers final: 20 residues processed: 189 average time/residue: 0.2866 time to fit residues: 78.2177 Evaluate side-chains 194 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 61 SER 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 F residue 85 ASP Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 170 PHE Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 687 MET Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 274 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16124 Z= 0.350 Angle : 0.613 10.910 23069 Z= 0.355 Chirality : 0.038 0.197 2643 Planarity : 0.004 0.043 1916 Dihedral : 29.317 176.339 4520 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.46 % Allowed : 15.95 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.25), residues: 1159 helix: 2.71 (0.19), residues: 736 sheet: 0.27 (0.73), residues: 48 loop : -0.41 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 52 HIS 0.017 0.001 HIS L 274 PHE 0.017 0.001 PHE L 273 TYR 0.038 0.002 TYR B 88 ARG 0.007 0.000 ARG L 271 ********************** 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 185 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7383 (mtp85) cc_final: 0.6884 (mpt180) REVERT: A 131 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8210 (mtt90) REVERT: B 63 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7853 (mt-10) REVERT: B 88 TYR cc_start: 0.8772 (m-10) cc_final: 0.8166 (m-10) REVERT: C 56 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8701 (tm-30) REVERT: C 64 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8476 (tm-30) REVERT: C 90 ASP cc_start: 0.8923 (t0) cc_final: 0.8685 (t0) REVERT: D 80 TYR cc_start: 0.8045 (m-10) cc_final: 0.7370 (m-10) REVERT: F 63 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7648 (tm-30) REVERT: G 90 ASP cc_start: 0.8200 (t0) cc_final: 0.7572 (t0) REVERT: G 100 VAL cc_start: 0.9758 (t) cc_final: 0.9457 (p) REVERT: H 68 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8476 (tp30) REVERT: K 54 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7274 (pm20) REVERT: K 226 ILE cc_start: 0.0403 (OUTLIER) cc_final: 0.0082 (tt) REVERT: K 231 MET cc_start: 0.8080 (mtm) cc_final: 0.7721 (mtt) REVERT: K 695 ASN cc_start: 0.8052 (t0) cc_final: 0.7575 (t0) REVERT: L 334 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8168 (mm-40) REVERT: L 336 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.8142 (tmt170) outliers start: 23 outliers final: 18 residues processed: 178 average time/residue: 0.2842 time to fit residues: 73.2555 Evaluate side-chains 180 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain D residue 61 SER 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 F residue 85 ASP Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 170 PHE Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain L residue 254 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 112 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 0.0000 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.091573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.058245 restraints weight = 56244.442| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.19 r_work: 0.2958 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3688 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= 0.169 Angle : 0.554 10.188 23069 Z= 0.323 Chirality : 0.035 0.194 2643 Planarity : 0.004 0.045 1916 Dihedral : 29.078 176.880 4520 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.93 % Allowed : 16.81 % Favored : 81.26 % 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: 2.69 (0.25), residues: 1159 helix: 2.88 (0.19), residues: 735 sheet: 0.40 (0.73), residues: 48 loop : -0.33 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 52 HIS 0.019 0.001 HIS L 274 PHE 0.009 0.001 PHE K 50 TYR 0.031 0.001 TYR K 241 ARG 0.007 0.000 ARG D 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.81 seconds wall clock time: 56 minutes 7.69 seconds (3367.69 seconds total)