Starting phenix.real_space_refine (version: dev) on Sat Jun 4 06:11:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcr_33126/06_2022/7xcr_33126_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcr_33126/06_2022/7xcr_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_33126/06_2022/7xcr_33126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcr_33126/06_2022/7xcr_33126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcr_33126/06_2022/7xcr_33126_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcr_33126/06_2022/7xcr_33126_updated.pdb" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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-4617/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: {'PTRANS': 18, 'CIS': 1, '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} 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} 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} Modifications used: {'COO': 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: 8.85, 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: 6.58 Conformation dependent library (CDL) restraints added in 1.5 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: 7.57 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: 6.19 Time building geometry restraints manager: 7.02 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=" N ILE K 48 " pdb=" CA ILE K 48 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.90e-02 2.77e+03 5.09e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.85e+00 bond pdb=" C ASN K 331 " pdb=" N PRO K 332 " ideal model delta sigma weight residual 1.341 1.374 -0.033 1.60e-02 3.91e+03 4.36e+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=" 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=" 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 angle pdb=" N PHE F 100 " pdb=" CA PHE F 100 " pdb=" C PHE F 100 " ideal model delta sigma weight residual 114.09 122.14 -8.05 1.55e+00 4.16e-01 2.70e+01 angle pdb=" C VAL F 57 " pdb=" N LEU F 58 " pdb=" CA LEU F 58 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.59e+01 ... (remaining 23254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 7530 35.46 - 70.91: 1272 70.91 - 106.37: 5 106.37 - 141.83: 1 141.83 - 177.28: 2 Dihedral angle restraints: 8810 sinusoidal: 5394 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 8807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2298 0.073 - 0.145: 278 0.145 - 0.218: 42 0.218 - 0.290: 4 0.290 - 0.362: 3 Chirality restraints: 2625 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 2622 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 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. 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: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 5.370 Check model and map are aligned: 0.240 Convert atoms to be neutral: 0.140 Process input model: 47.780 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:15.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.007 0.077 16287 Z= 0.443 Angle : 0.957 15.023 23259 Z= 0.537 Chirality : 0.053 0.362 2625 Planarity : 0.007 0.069 1940 Dihedral : 23.884 177.284 6604 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer Outliers : 0.90 % 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 *********************** 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 : 1.698 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 262 average time/residue: 1.8114 time to fit residues: 507.6860 Evaluate side-chains 175 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.2674 time to fit residues: 2.0095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 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: 0.8980 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 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: 0.8200 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16287 Z= 0.194 Angle : 0.662 18.620 23259 Z= 0.374 Chirality : 0.039 0.162 2625 Planarity : 0.005 0.058 1940 Dihedral : 29.118 177.907 4257 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.52 % Rotamer Outliers : 3.10 % 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: -1.90 (0.22), residues: 1148 helix: -1.35 (0.17), residues: 662 sheet: -0.60 (0.57), residues: 82 loop : -0.89 (0.29), residues: 404 *********************** 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 209 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 1.354 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 13 residues processed: 195 average time/residue: 1.6254 time to fit residues: 342.4502 Evaluate side-chains 177 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 164 time to evaluate : 1.298 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.1828 time to fit residues: 3.2098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 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: 9.9990 chunk 101 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 47 GLN H 84 ASN H 109 HIS ** 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: 0.8334 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.071 16287 Z= 0.549 Angle : 0.815 18.512 23259 Z= 0.452 Chirality : 0.051 0.256 2625 Planarity : 0.007 0.052 1940 Dihedral : 29.553 172.278 4257 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.48 % Favored : 96.25 % Rotamer Outliers : 4.00 % 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: -0.95 (0.24), residues: 1148 helix: -0.43 (0.19), residues: 676 sheet: -0.34 (0.59), residues: 81 loop : -0.78 (0.30), residues: 391 *********************** 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 209 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 1.250 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 25 residues processed: 192 average time/residue: 1.6407 time to fit residues: 339.5199 Evaluate side-chains 188 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 15 residues processed: 10 average time/residue: 0.7664 time to fit residues: 10.5547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 84 optimal weight: 0.0270 chunk 126 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.9444 ------------------------------------------------------------------------------- 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 D 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 16287 Z= 0.204 Angle : 0.666 18.609 23259 Z= 0.378 Chirality : 0.040 0.162 2625 Planarity : 0.004 0.055 1940 Dihedral : 29.553 175.360 4257 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.75 % Favored : 95.99 % Rotamer Outliers : 3.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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 (0.25), residues: 1148 helix: 0.31 (0.20), residues: 674 sheet: -0.15 (0.60), residues: 81 loop : -0.55 (0.30), residues: 393 *********************** 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: 36 poor density : 167 time to evaluate : 1.204 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 191 average time/residue: 1.5984 time to fit residues: 330.2338 Evaluate side-chains 183 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 17 residues processed: 8 average time/residue: 1.0554 time to fit residues: 11.0671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 16287 Z= 0.374 Angle : 0.703 18.600 23259 Z= 0.396 Chirality : 0.044 0.202 2625 Planarity : 0.005 0.051 1940 Dihedral : 29.532 175.285 4257 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer Outliers : 4.40 % 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: 0.05 (0.25), residues: 1148 helix: 0.46 (0.20), residues: 677 sheet: -0.23 (0.59), residues: 81 loop : -0.45 (0.30), residues: 390 *********************** 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 201 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 157 time to evaluate : 1.404 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 28 residues processed: 185 average time/residue: 1.6320 time to fit residues: 326.4052 Evaluate side-chains 185 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 18 residues processed: 10 average time/residue: 0.7726 time to fit residues: 10.5350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 16287 Z= 0.265 Angle : 0.678 18.599 23259 Z= 0.383 Chirality : 0.041 0.261 2625 Planarity : 0.005 0.052 1940 Dihedral : 29.534 175.651 4257 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.92 % Favored : 95.82 % Rotamer Outliers : 3.00 % 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: 0.32 (0.25), residues: 1148 helix: 0.69 (0.21), residues: 677 sheet: -0.14 (0.60), residues: 81 loop : -0.36 (0.31), residues: 390 *********************** 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 190 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.383 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 26 residues processed: 183 average time/residue: 1.6085 time to fit residues: 317.7222 Evaluate side-chains 184 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 6 average time/residue: 1.1272 time to fit residues: 8.9402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2873 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 : 0.725 18.466 23259 Z= 0.408 Chirality : 0.045 0.219 2625 Planarity : 0.005 0.049 1940 Dihedral : 29.620 174.461 4257 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.92 % Favored : 95.82 % Rotamer Outliers : 4.40 % 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: 0.17 (0.25), residues: 1148 helix: 0.57 (0.20), residues: 678 sheet: -0.29 (0.61), residues: 81 loop : -0.41 (0.31), residues: 389 *********************** 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 204 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 160 time to evaluate : 1.211 Fit side-chains outliers start: 44 outliers final: 29 residues processed: 188 average time/residue: 1.6142 time to fit residues: 330.0441 Evaluate side-chains 187 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.374 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 19 residues processed: 10 average time/residue: 0.9839 time to fit residues: 12.8436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 105 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16287 Z= 0.186 Angle : 0.621 18.638 23259 Z= 0.352 Chirality : 0.037 0.158 2625 Planarity : 0.004 0.049 1940 Dihedral : 29.283 178.900 4257 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.91 % Rotamer Outliers : 3.20 % 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: 0.76 (0.25), residues: 1148 helix: 1.07 (0.21), residues: 673 sheet: -0.00 (0.61), residues: 80 loop : -0.21 (0.31), residues: 395 *********************** 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 196 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.461 Fit side-chains outliers start: 32 outliers final: 23 residues processed: 185 average time/residue: 1.5692 time to fit residues: 314.0899 Evaluate side-chains 184 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.385 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.5010 time to fit residues: 4.8555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN D 67 ASN C 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2991 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= 0.414 Angle : 0.719 18.446 23259 Z= 0.403 Chirality : 0.045 0.213 2625 Planarity : 0.005 0.044 1940 Dihedral : 29.538 175.227 4257 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.82 % Rotamer Outliers : 2.90 % 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: 0.39 (0.25), residues: 1148 helix: 0.73 (0.20), residues: 684 sheet: -0.16 (0.60), residues: 81 loop : -0.32 (0.32), residues: 383 *********************** 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 191 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.336 Fit side-chains outliers start: 29 outliers final: 23 residues processed: 183 average time/residue: 1.6362 time to fit residues: 323.4002 Evaluate side-chains 184 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.8321 time to fit residues: 6.2565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 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 ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 16287 Z= 0.198 Angle : 0.640 18.827 23259 Z= 0.361 Chirality : 0.038 0.179 2625 Planarity : 0.004 0.046 1940 Dihedral : 29.459 177.495 4257 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.08 % Rotamer Outliers : 2.40 % 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: 0.79 (0.25), residues: 1148 helix: 1.08 (0.21), residues: 681 sheet: 0.10 (0.61), residues: 80 loop : -0.24 (0.32), residues: 387 ********************** 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 189 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.401 Fit side-chains outliers start: 24 outliers final: 23 residues processed: 185 average time/residue: 1.6125 time to fit residues: 321.6708 Evaluate side-chains 185 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.361 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 4 average time/residue: 0.8439 time to fit residues: 5.5353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN D 67 ASN C 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.167001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133308 restraints weight = 17327.090| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.09 r_work: 0.3616 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.3588 rms_B_bonded: 1.16 restraints_weight: 0.1250 r_work: 0.3573 rms_B_bonded: 1.32 restraints_weight: 0.0625 r_work: 0.3557 rms_B_bonded: 1.53 restraints_weight: 0.0312 r_work: 0.3540 rms_B_bonded: 1.78 restraints_weight: 0.0156 r_work: 0.3521 rms_B_bonded: 2.07 restraints_weight: 0.0078 r_work: 0.3499 rms_B_bonded: 2.42 restraints_weight: 0.0039 r_work: 0.3475 rms_B_bonded: 2.83 restraints_weight: 0.0020 r_work: 0.3448 rms_B_bonded: 3.31 restraints_weight: 0.0010 r_work: 0.3417 rms_B_bonded: 3.86 restraints_weight: 0.0005 r_work: 0.3383 rms_B_bonded: 4.52 restraints_weight: 0.0002 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 16287 Z= 0.266 Angle : 0.651 18.748 23259 Z= 0.368 Chirality : 0.040 0.193 2625 Planarity : 0.004 0.045 1940 Dihedral : 29.352 177.421 4257 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.91 % Rotamer Outliers : 2.60 % 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 (0.26), residues: 1148 helix: 1.06 (0.21), residues: 683 sheet: 0.16 (0.61), residues: 80 loop : -0.18 (0.32), residues: 385 =============================================================================== Job complete usr+sys time: 5170.54 seconds wall clock time: 92 minutes 19.52 seconds (5539.52 seconds total)