Starting phenix.real_space_refine on Mon Mar 18 15:15:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcr_33126/03_2024/7xcr_33126_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcr_33126/03_2024/7xcr_33126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcr_33126/03_2024/7xcr_33126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcr_33126/03_2024/7xcr_33126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcr_33126/03_2024/7xcr_33126_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcr_33126/03_2024/7xcr_33126_updated.pdb" } resolution = 2.57 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= -0.001 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic. 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 292 5.49 5 S 26 5.16 5 C 8789 2.51 5 N 2847 2.21 5 O 3446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 278": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" 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: 15400 Number of models: 1 Model: "" Number of chains: 13 Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "K" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2671 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 308} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 residue: pdb=" N GLY L 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY L 76 " occ=0.25 Time building chain proxies: 8.84, per 1000 atoms: 0.57 Number of scatterers: 15400 At special positions: 0 Unit cell: (120.96, 122.04, 130.68, 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 26 16.00 P 292 15.00 O 3446 8.00 N 2847 7.00 C 8789 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: 7.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 2 sheets defined 48.3% alpha, 3.6% beta 135 base pairs and 277 stacking pairs defined. Time for finding SS restraints: 7.47 Creating SS restraints... Processing helix chain 'L' and resid 23 through 33 removed outlier: 4.048A pdb=" N GLN L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'F' and resid 31 through 34 No H-bonds generated for 'chain 'F' and resid 31 through 34' Processing helix chain 'F' and resid 50 through 56 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.524A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'H' and resid 38 through 48 removed outlier: 3.699A pdb=" N LYS H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 83 removed outlier: 3.616A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 105 through 121 Processing helix chain 'K' and resid 35 through 45 removed outlier: 4.028A pdb=" N ARG K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 54 No H-bonds generated for 'chain 'K' and resid 51 through 54' Processing helix chain 'K' and resid 68 through 89 removed outlier: 3.610A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS K 77 " --> pdb=" O ARG K 73 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASP K 83 " --> pdb=" O ASN K 79 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE K 85 " --> pdb=" O ALA K 81 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN K 87 " --> pdb=" O ASP K 83 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU K 88 " --> pdb=" O SER K 84 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TRP K 89 " --> pdb=" O ILE K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 118 Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'K' and resid 141 through 150 Processing helix chain 'K' and resid 168 through 174 removed outlier: 3.524A pdb=" N GLN K 172 " --> pdb=" O GLN K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 207 removed outlier: 3.709A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG K 203 " --> pdb=" O ASP K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 233 removed outlier: 4.376A pdb=" N GLU K 230 " --> pdb=" O GLU K 226 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 259 removed outlier: 3.506A pdb=" N GLN K 252 " --> pdb=" O GLU K 248 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU K 255 " --> pdb=" O HIS K 251 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN K 259 " --> pdb=" O GLU K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 289 No H-bonds generated for 'chain 'K' and resid 287 through 289' Processing helix chain 'K' and resid 322 through 328 removed outlier: 3.591A pdb=" N SER K 328 " --> pdb=" O ASN K 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.514A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.611A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.602A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 removed outlier: 3.564A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.524A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 93 through 96 No H-bonds generated for 'chain 'C' and resid 93 through 96' Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.628A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.820A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'L' and resid 12 through 16 Processing sheet with id= B, first strand: chain 'K' and resid 291 through 295 removed outlier: 4.108A pdb=" N PHE K 159 " --> pdb=" O HIS K 181 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU K 215 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N GLY K 184 " --> pdb=" O GLU K 215 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR K 217 " --> pdb=" O GLY K 184 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N GLU K 186 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU K 219 " --> pdb=" O GLU K 186 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 338 hydrogen bonds 668 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 277 stacking parallelities Total time for adding SS restraints: 8.18 Time building geometry restraints manager: 8.24 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: 2831 1.33 - 1.45: 5088 1.45 - 1.57: 7738 1.57 - 1.69: 582 1.69 - 1.81: 48 Bond restraints: 16287 Sorted by residual: bond pdb=" C ALA F 69 " pdb=" N VAL F 70 " ideal model delta sigma weight residual 1.335 1.298 0.036 1.16e-02 7.43e+03 9.90e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.64e+00 bond pdb=" C2 SAM K 500 " pdb=" N3 SAM K 500 " ideal model delta sigma weight residual 1.322 1.373 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C2 SAM K 500 " pdb=" N1 SAM K 500 " ideal model delta sigma weight residual 1.329 1.378 -0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" C8 SAM K 500 " pdb=" N7 SAM K 500 " ideal model delta sigma weight residual 1.298 1.346 -0.048 2.00e-02 2.50e+03 5.72e+00 ... (remaining 16282 not shown) Histogram of bond angle deviations from ideal: 98.04 - 106.44: 2117 106.44 - 114.83: 9547 114.83 - 123.23: 9887 123.23 - 131.63: 1625 131.63 - 140.02: 83 Bond angle restraints: 23259 Sorted by residual: angle pdb=" C GLU K 47 " pdb=" N ILE K 48 " pdb=" CA ILE K 48 " ideal model delta sigma weight residual 121.70 137.69 -15.99 1.80e+00 3.09e-01 7.89e+01 angle pdb=" N LEU F 37 " pdb=" CA LEU F 37 " pdb=" C LEU F 37 " ideal model delta sigma weight residual 114.75 104.75 10.00 1.26e+00 6.30e-01 6.30e+01 angle pdb=" C ARG F 67 " pdb=" N ASP F 68 " pdb=" CA ASP F 68 " ideal model delta sigma weight residual 121.54 134.44 -12.90 1.91e+00 2.74e-01 4.56e+01 angle pdb=" C PHE F 100 " pdb=" N GLY F 101 " pdb=" CA GLY F 101 " ideal model delta sigma weight residual 121.70 133.06 -11.36 1.80e+00 3.09e-01 3.98e+01 angle pdb=" CA PHE F 100 " pdb=" C PHE F 100 " pdb=" N GLY F 101 " ideal model delta sigma weight residual 119.07 125.58 -6.51 1.23e+00 6.61e-01 2.81e+01 ... (remaining 23254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 7784 35.46 - 70.91: 1291 70.91 - 106.37: 5 106.37 - 141.83: 1 141.83 - 177.28: 2 Dihedral angle restraints: 9083 sinusoidal: 5667 harmonic: 3416 Sorted by residual: dihedral pdb=" CA GLN F 27 " pdb=" C GLN F 27 " pdb=" N GLY F 28 " pdb=" CA GLY F 28 " ideal model delta harmonic sigma weight residual 180.00 116.95 63.05 0 5.00e+00 4.00e-02 1.59e+02 dihedral pdb=" CA VAL F 57 " pdb=" C VAL F 57 " pdb=" N LEU F 58 " pdb=" CA LEU F 58 " ideal model delta harmonic sigma weight residual -180.00 -138.91 -41.09 0 5.00e+00 4.00e-02 6.75e+01 dihedral pdb=" CA ASP K 32 " pdb=" C ASP K 32 " pdb=" N ALA K 33 " pdb=" CA ALA K 33 " ideal model delta harmonic sigma weight residual -180.00 -142.61 -37.39 0 5.00e+00 4.00e-02 5.59e+01 ... (remaining 9080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2296 0.073 - 0.145: 280 0.145 - 0.218: 43 0.218 - 0.290: 4 0.290 - 0.362: 3 Chirality restraints: 2626 Sorted by residual: chirality pdb=" CB ILE C 79 " pdb=" CA ILE C 79 " pdb=" CG1 ILE C 79 " pdb=" CG2 ILE C 79 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB ILE G 79 " pdb=" CA ILE G 79 " pdb=" CG1 ILE G 79 " pdb=" CG2 ILE G 79 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CB VAL F 43 " pdb=" CA VAL F 43 " pdb=" CG1 VAL F 43 " pdb=" CG2 VAL F 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2623 not shown) Planarity restraints: 1940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 57 " -0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C VAL F 57 " 0.074 2.00e-02 2.50e+03 pdb=" O VAL F 57 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU F 58 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " 0.024 2.00e-02 2.50e+03 2.15e-02 8.07e+00 pdb=" CG PHE G 25 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 25 " -0.024 2.00e-02 2.50e+03 2.14e-02 8.02e+00 pdb=" CG PHE C 25 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE C 25 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 25 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 25 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 25 " -0.008 2.00e-02 2.50e+03 ... (remaining 1937 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2354 2.76 - 3.30: 12612 3.30 - 3.83: 28518 3.83 - 4.37: 36724 4.37 - 4.90: 52239 Nonbonded interactions: 132447 Sorted by model distance: nonbonded pdb=" OG1 THR F 82 " pdb=" O MET F 84 " model vdw 2.228 2.440 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.287 2.440 nonbonded pdb=" OG1 THR K 154 " pdb=" OD1 ASP K 156 " model vdw 2.302 2.440 nonbonded pdb=" O GLU K 36 " pdb=" OG1 THR K 40 " model vdw 2.341 2.440 nonbonded pdb=" NH2 ARG F 78 " pdb=" OD2 ASP F 85 " model vdw 2.342 2.520 ... (remaining 132442 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 38 through 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } 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=0.25 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: 0.010 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 4.450 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 52.580 Find NCS groups from input model: 0.550 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:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.008 0.077 16287 Z= 0.445 Angle : 0.969 15.994 23259 Z= 0.543 Chirality : 0.053 0.362 2626 Planarity : 0.007 0.069 1940 Dihedral : 23.821 177.284 6877 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 0.90 % Allowed : 3.40 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.89 % 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: -4.82 (0.18), residues: 1148 helix: -4.10 (0.09), residues: 665 sheet: -1.34 (0.51), residues: 80 loop : -1.44 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP K 89 HIS 0.015 0.003 HIS B 75 PHE 0.049 0.004 PHE G 25 TYR 0.031 0.003 TYR K 312 ARG 0.016 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 255 time to evaluate : 1.546 Fit side-chains REVERT: F 53 GLU cc_start: 0.8495 (tp30) cc_final: 0.8279 (tp30) REVERT: H 54 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.7999 (mt) REVERT: H 71 GLU cc_start: 0.7217 (pp20) cc_final: 0.6872 (pp20) REVERT: A 50 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7951 (mt-10) REVERT: B 52 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7751 (mm-30) outliers start: 9 outliers final: 4 residues processed: 262 average time/residue: 1.9545 time to fit residues: 544.3698 Evaluate side-chains 175 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain B residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 60 ASN F 18 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 24 GLN G 82 HIS G 94 ASN G 110 ASN H 63 ASN K 79 ASN K 86 HIS K 146 GLN K 234 ASN K 324 ASN E 76 GLN E 85 GLN A 39 HIS A 68 GLN D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS C 24 GLN C 82 HIS B 25 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16287 Z= 0.198 Angle : 0.653 12.395 23259 Z= 0.377 Chirality : 0.039 0.184 2626 Planarity : 0.005 0.060 1940 Dihedral : 28.624 178.017 4538 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 2.80 % Allowed : 11.21 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.22), residues: 1148 helix: -1.44 (0.17), residues: 662 sheet: -0.64 (0.56), residues: 82 loop : -0.89 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 89 HIS 0.004 0.001 HIS K 315 PHE 0.017 0.002 PHE K 223 TYR 0.010 0.001 TYR F 72 ARG 0.005 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7219 (pp20) cc_final: 0.6917 (pp20) REVERT: K 113 GLN cc_start: 0.8293 (tt0) cc_final: 0.8046 (tt0) REVERT: D 99 ARG cc_start: 0.8148 (mtt90) cc_final: 0.7945 (mtt180) outliers start: 28 outliers final: 14 residues processed: 192 average time/residue: 1.6587 time to fit residues: 342.1177 Evaluate side-chains 178 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 51 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 105 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 84 ASN H 109 HIS D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 16287 Z= 0.494 Angle : 0.774 12.211 23259 Z= 0.438 Chirality : 0.049 0.233 2626 Planarity : 0.006 0.053 1940 Dihedral : 29.091 172.541 4536 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.66 % Favored : 96.08 % Rotamer: Outliers : 4.00 % Allowed : 11.41 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -0.89 (0.24), residues: 1148 helix: -0.40 (0.19), residues: 676 sheet: -0.31 (0.59), residues: 81 loop : -0.71 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP K 205 HIS 0.009 0.002 HIS F 75 PHE 0.027 0.003 PHE G 25 TYR 0.018 0.002 TYR K 312 ARG 0.008 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 173 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7784 (mt) REVERT: F 92 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8178 (ttp80) REVERT: H 99 ARG cc_start: 0.8325 (mtm110) cc_final: 0.8091 (mtm180) REVERT: K 206 MET cc_start: 0.8319 (mmp) cc_final: 0.7970 (mmt) REVERT: D 99 ARG cc_start: 0.8208 (mtt90) cc_final: 0.7952 (mtt180) REVERT: C 64 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7778 (tt0) outliers start: 40 outliers final: 25 residues processed: 195 average time/residue: 1.7759 time to fit residues: 370.6764 Evaluate side-chains 189 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16287 Z= 0.235 Angle : 0.629 12.241 23259 Z= 0.365 Chirality : 0.039 0.182 2626 Planarity : 0.004 0.054 1940 Dihedral : 28.836 177.334 4536 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.48 % Favored : 96.25 % Rotamer: Outliers : 3.40 % Allowed : 12.81 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -0.04 (0.25), residues: 1148 helix: 0.34 (0.20), residues: 673 sheet: -0.14 (0.60), residues: 81 loop : -0.43 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 205 HIS 0.004 0.001 HIS K 315 PHE 0.014 0.001 PHE K 223 TYR 0.012 0.001 TYR D 40 ARG 0.006 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7621 (mt) REVERT: G 64 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: H 57 LYS cc_start: 0.8881 (tptt) cc_final: 0.8673 (tptp) REVERT: D 99 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7862 (mtt180) outliers start: 34 outliers final: 23 residues processed: 189 average time/residue: 1.7094 time to fit residues: 347.0150 Evaluate side-chains 185 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS K 234 ASN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 16287 Z= 0.459 Angle : 0.734 12.168 23259 Z= 0.420 Chirality : 0.047 0.234 2626 Planarity : 0.006 0.049 1940 Dihedral : 29.156 173.744 4536 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 4.00 % Allowed : 13.71 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -0.13 (0.24), residues: 1148 helix: 0.28 (0.20), residues: 677 sheet: -0.25 (0.59), residues: 81 loop : -0.47 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP K 205 HIS 0.007 0.001 HIS F 75 PHE 0.018 0.002 PHE G 25 TYR 0.011 0.002 TYR K 312 ARG 0.005 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 159 time to evaluate : 1.207 Fit side-chains REVERT: F 90 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7825 (mt) REVERT: K 170 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8647 (t) REVERT: K 206 MET cc_start: 0.8455 (mmt) cc_final: 0.8103 (mmt) REVERT: D 99 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7910 (mtt180) REVERT: C 64 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: B 95 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.6236 (mmp80) outliers start: 40 outliers final: 31 residues processed: 185 average time/residue: 1.7078 time to fit residues: 338.9492 Evaluate side-chains 193 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS E 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16287 Z= 0.212 Angle : 0.641 12.212 23259 Z= 0.373 Chirality : 0.039 0.177 2626 Planarity : 0.004 0.052 1940 Dihedral : 29.075 175.877 4536 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 95.99 % Rotamer: Outliers : 3.50 % Allowed : 14.71 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: 0.41 (0.25), residues: 1148 helix: 0.75 (0.21), residues: 674 sheet: -0.11 (0.60), residues: 81 loop : -0.28 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 205 HIS 0.005 0.001 HIS K 315 PHE 0.014 0.001 PHE K 223 TYR 0.013 0.001 TYR D 40 ARG 0.005 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 1.303 Fit side-chains REVERT: F 90 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7712 (mt) REVERT: C 64 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: C 95 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8189 (ttmt) REVERT: B 95 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.6194 (mmp80) outliers start: 35 outliers final: 24 residues processed: 185 average time/residue: 1.7355 time to fit residues: 345.1767 Evaluate side-chains 189 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16287 Z= 0.331 Angle : 0.671 12.157 23259 Z= 0.387 Chirality : 0.042 0.229 2626 Planarity : 0.005 0.049 1940 Dihedral : 29.006 175.563 4536 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 95.99 % Rotamer: Outliers : 3.90 % Allowed : 14.91 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: 0.41 (0.25), residues: 1148 helix: 0.74 (0.20), residues: 677 sheet: -0.10 (0.59), residues: 81 loop : -0.27 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 205 HIS 0.005 0.001 HIS F 75 PHE 0.014 0.002 PHE K 223 TYR 0.011 0.002 TYR D 40 ARG 0.004 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 162 time to evaluate : 1.392 Fit side-chains REVERT: F 90 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7768 (mt) REVERT: K 101 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7169 (mtt-85) REVERT: C 64 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: C 95 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8187 (ttmt) REVERT: B 95 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.6180 (mmp80) outliers start: 39 outliers final: 31 residues processed: 184 average time/residue: 1.7340 time to fit residues: 342.0414 Evaluate side-chains 197 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 101 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16287 Z= 0.202 Angle : 0.632 12.193 23259 Z= 0.367 Chirality : 0.038 0.188 2626 Planarity : 0.004 0.050 1940 Dihedral : 28.986 176.640 4536 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.73 % Rotamer: Outliers : 4.00 % Allowed : 14.51 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: 0.69 (0.25), residues: 1148 helix: 0.99 (0.21), residues: 674 sheet: 0.07 (0.60), residues: 81 loop : -0.21 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 205 HIS 0.004 0.001 HIS K 315 PHE 0.013 0.001 PHE K 223 TYR 0.013 0.001 TYR D 40 ARG 0.006 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 162 time to evaluate : 1.194 Fit side-chains REVERT: F 90 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7696 (mt) REVERT: H 57 LYS cc_start: 0.8958 (tptt) cc_final: 0.8747 (mptp) REVERT: C 64 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: C 95 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8052 (ttmt) REVERT: B 95 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.6153 (mmp80) outliers start: 40 outliers final: 27 residues processed: 187 average time/residue: 1.7036 time to fit residues: 342.3958 Evaluate side-chains 192 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 0.0470 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 16287 Z= 0.415 Angle : 0.711 12.185 23259 Z= 0.407 Chirality : 0.045 0.217 2626 Planarity : 0.005 0.044 1940 Dihedral : 29.112 174.642 4536 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.82 % Rotamer: Outliers : 4.00 % Allowed : 14.21 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: 0.37 (0.25), residues: 1148 helix: 0.69 (0.20), residues: 683 sheet: -0.04 (0.59), residues: 80 loop : -0.30 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP K 205 HIS 0.006 0.001 HIS K 315 PHE 0.016 0.002 PHE K 223 TYR 0.011 0.002 TYR B 88 ARG 0.007 0.001 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 161 time to evaluate : 1.451 Fit side-chains REVERT: F 90 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7832 (mt) REVERT: K 101 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7217 (mtt-85) REVERT: C 64 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: C 95 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8181 (ttmt) REVERT: B 95 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.6972 (mtp180) outliers start: 40 outliers final: 32 residues processed: 187 average time/residue: 1.8790 time to fit residues: 378.2113 Evaluate side-chains 198 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 161 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 101 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16287 Z= 0.210 Angle : 0.647 12.190 23259 Z= 0.375 Chirality : 0.039 0.184 2626 Planarity : 0.004 0.047 1940 Dihedral : 29.075 175.789 4536 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.92 % Favored : 95.82 % Rotamer: Outliers : 3.60 % Allowed : 14.71 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: 0.66 (0.25), residues: 1148 helix: 0.94 (0.21), residues: 682 sheet: 0.11 (0.60), residues: 80 loop : -0.21 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 205 HIS 0.004 0.001 HIS K 315 PHE 0.013 0.001 PHE K 223 TYR 0.015 0.001 TYR D 40 ARG 0.007 0.001 ARG H 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 1.319 Fit side-chains REVERT: F 90 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7752 (mt) REVERT: K 101 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7129 (mtt-85) REVERT: C 64 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: C 95 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8190 (ttmt) outliers start: 36 outliers final: 28 residues processed: 184 average time/residue: 1.7367 time to fit residues: 342.9295 Evaluate side-chains 195 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 101 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 4.9990 chunk 101 optimal weight: 0.0970 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 13 optimal weight: 0.0870 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.4360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS E 125 GLN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.166617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133149 restraints weight = 17386.167| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.07 r_work: 0.3481 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16287 Z= 0.237 Angle : 0.633 12.243 23259 Z= 0.366 Chirality : 0.039 0.189 2626 Planarity : 0.004 0.045 1940 Dihedral : 28.913 177.257 4536 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.91 % Rotamer: Outliers : 3.30 % Allowed : 15.22 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: 0.80 (0.25), residues: 1148 helix: 1.06 (0.21), residues: 680 sheet: 0.17 (0.60), residues: 80 loop : -0.16 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 205 HIS 0.004 0.001 HIS K 315 PHE 0.015 0.001 PHE K 223 TYR 0.012 0.001 TYR D 40 ARG 0.006 0.000 ARG H 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5900.00 seconds wall clock time: 104 minutes 19.10 seconds (6259.10 seconds total)