Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 03:45:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xla_22237/10_2023/6xla_22237_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xla_22237/10_2023/6xla_22237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xla_22237/10_2023/6xla_22237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xla_22237/10_2023/6xla_22237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xla_22237/10_2023/6xla_22237_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xla_22237/10_2023/6xla_22237_updated.pdb" } resolution = 3.1 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Sb 2 10.97 5 P 44 5.49 5 S 26 5.16 5 C 3339 2.51 5 N 912 2.21 5 O 1080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "G TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 135": "OD1" <-> "OD2" Residue "G ASP 171": "OD1" <-> "OD2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 217": "OD1" <-> "OD2" Residue "G GLU 231": "OE1" <-> "OE2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 44": "OD1" <-> "OD2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 171": "OD1" <-> "OD2" Residue "H GLU 185": "OE1" <-> "OE2" Residue "H PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 220": "NH1" <-> "NH2" Residue "H TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 254": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 5403 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "H" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "N" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "T" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 467 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'118': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'118': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.65, per 1000 atoms: 0.68 Number of scatterers: 5403 At special positions: 0 Unit cell: (116.35, 104.715, 71.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Sb 2 50.95 S 26 16.00 P 44 15.00 O 1080 8.00 N 912 7.00 C 3339 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: 2.38 Conformation dependent library (CDL) restraints added in 645.4 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1028 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 3 sheets defined 41.6% alpha, 18.5% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'G' and resid 4 through 10 removed outlier: 3.607A pdb=" N LYS G 9 " --> pdb=" O GLY G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 24 Processing helix chain 'G' and resid 43 through 58 removed outlier: 3.788A pdb=" N GLN G 51 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 75 through 109 removed outlier: 4.097A pdb=" N GLU G 79 " --> pdb=" O HIS G 76 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG G 80 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU G 83 " --> pdb=" O ARG G 80 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE G 85 " --> pdb=" O ARG G 82 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS G 87 " --> pdb=" O GLU G 84 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE G 89 " --> pdb=" O GLN G 86 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU G 96 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE G 99 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU G 103 " --> pdb=" O ASN G 100 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LYS G 107 " --> pdb=" O GLN G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 Proline residue: G 144 - end of helix removed outlier: 3.594A pdb=" N VAL G 150 " --> pdb=" O ILE G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 232 removed outlier: 5.577A pdb=" N ARG G 220 " --> pdb=" O ASP G 217 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE G 224 " --> pdb=" O ASN G 221 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET G 227 " --> pdb=" O ILE G 224 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL G 230 " --> pdb=" O MET G 227 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP G 232 " --> pdb=" O TRP G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 257 No H-bonds generated for 'chain 'G' and resid 255 through 257' Processing helix chain 'H' and resid 4 through 11 removed outlier: 3.646A pdb=" N LYS H 9 " --> pdb=" O GLY H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 24 Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.919A pdb=" N GLN H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU H 58 " --> pdb=" O SER H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 70 removed outlier: 4.039A pdb=" N GLN H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 108 removed outlier: 3.722A pdb=" N GLU H 84 " --> pdb=" O ARG H 80 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN H 86 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS H 108 " --> pdb=" O GLN H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 142 Processing helix chain 'H' and resid 144 through 153 removed outlier: 3.710A pdb=" N VAL H 150 " --> pdb=" O ILE H 146 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET H 151 " --> pdb=" O GLY H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 232 removed outlier: 4.263A pdb=" N ARG H 220 " --> pdb=" O ASP H 217 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU H 226 " --> pdb=" O TYR H 223 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL H 230 " --> pdb=" O MET H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing sheet with id= A, first strand: chain 'G' and resid 117 through 121 removed outlier: 6.850A pdb=" N GLU G 261 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N TYR G 245 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLN G 263 " --> pdb=" O GLU G 243 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLU G 243 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N CYS G 165 " --> pdb=" O TYR G 245 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 235 through 237 Processing sheet with id= C, first strand: chain 'H' and resid 117 through 121 removed outlier: 6.949A pdb=" N GLU H 261 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TYR H 245 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLN H 263 " --> pdb=" O GLU H 243 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLU H 243 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N CYS H 165 " --> pdb=" O TYR H 245 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 435 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 2328 1.40 - 1.58: 3160 1.58 - 1.77: 88 1.77 - 1.95: 42 1.95 - 2.13: 8 Bond restraints: 5626 Sorted by residual: bond pdb="SB 118 G 301 " pdb=" C1C 118 G 301 " ideal model delta sigma weight residual 2.092 2.134 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb="SB 118 G 301 " pdb=" C1D 118 G 301 " ideal model delta sigma weight residual 2.092 2.131 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb="SB 118 H 301 " pdb=" C1C 118 H 301 " ideal model delta sigma weight residual 2.092 2.130 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb="SB 118 H 301 " pdb=" C1D 118 H 301 " ideal model delta sigma weight residual 2.092 2.129 -0.037 2.00e-02 2.50e+03 3.38e+00 bond pdb="SB 118 G 301 " pdb=" C1A 118 G 301 " ideal model delta sigma weight residual 2.093 2.129 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 5621 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.60: 419 106.60 - 113.45: 2996 113.45 - 120.31: 2185 120.31 - 127.16: 2083 127.16 - 134.02: 130 Bond angle restraints: 7813 Sorted by residual: angle pdb=" N ILE G 143 " pdb=" CA ILE G 143 " pdb=" C ILE G 143 " ideal model delta sigma weight residual 108.88 117.04 -8.16 2.16e+00 2.14e-01 1.43e+01 angle pdb=" N PRO H 144 " pdb=" CA PRO H 144 " pdb=" C PRO H 144 " ideal model delta sigma weight residual 110.70 115.28 -4.58 1.22e+00 6.72e-01 1.41e+01 angle pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " pdb=" P DT N 62 " ideal model delta sigma weight residual 120.20 124.33 -4.13 1.50e+00 4.44e-01 7.60e+00 angle pdb=" CA ILE G 143 " pdb=" C ILE G 143 " pdb=" N PRO G 144 " ideal model delta sigma weight residual 118.88 122.79 -3.91 1.54e+00 4.22e-01 6.44e+00 angle pdb=" N ILE H 143 " pdb=" CA ILE H 143 " pdb=" C ILE H 143 " ideal model delta sigma weight residual 108.88 114.23 -5.35 2.16e+00 2.14e-01 6.14e+00 ... (remaining 7808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.48: 2936 31.48 - 62.95: 245 62.95 - 94.43: 14 94.43 - 125.91: 0 125.91 - 157.38: 1 Dihedral angle restraints: 3196 sinusoidal: 1600 harmonic: 1596 Sorted by residual: dihedral pdb=" CA VAL H 126 " pdb=" C VAL H 126 " pdb=" N TYR H 127 " pdb=" CA TYR H 127 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ILE H 143 " pdb=" C ILE H 143 " pdb=" N PRO H 144 " pdb=" CA PRO H 144 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C4' DT N 61 " pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " pdb=" P DT N 62 " ideal model delta sinusoidal sigma weight residual 220.00 62.62 157.38 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 3193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 493 0.031 - 0.063: 250 0.063 - 0.094: 75 0.094 - 0.125: 24 0.125 - 0.156: 12 Chirality restraints: 854 Sorted by residual: chirality pdb=" CA ILE H 132 " pdb=" N ILE H 132 " pdb=" C ILE H 132 " pdb=" CB ILE H 132 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA VAL H 210 " pdb=" N VAL H 210 " pdb=" C VAL H 210 " pdb=" CB VAL H 210 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CB ILE G 143 " pdb=" CA ILE G 143 " pdb=" CG1 ILE G 143 " pdb=" CG2 ILE G 143 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 851 not shown) Planarity restraints: 832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 144 " 0.041 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO H 145 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO H 145 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 145 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 51 " -0.024 2.00e-02 2.50e+03 1.01e-02 2.82e+00 pdb=" N9 DA N 51 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA N 51 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA N 51 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA N 51 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA N 51 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA N 51 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA N 51 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA N 51 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA N 51 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA N 51 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO G 144 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO G 145 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO G 145 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 145 " 0.023 5.00e-02 4.00e+02 ... (remaining 829 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1293 2.80 - 3.33: 4466 3.33 - 3.85: 8574 3.85 - 4.38: 10714 4.38 - 4.90: 16596 Nonbonded interactions: 41643 Sorted by model distance: nonbonded pdb=" OH TYR G 127 " pdb=" OE1 GLU G 185 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR H 61 " pdb=" OE1 GLU H 64 " model vdw 2.288 2.440 nonbonded pdb=" OG1 THR G 61 " pdb=" OE2 GLU G 64 " model vdw 2.305 2.440 nonbonded pdb=" N6 DA N 51 " pdb=" O4 DT T 38 " model vdw 2.332 2.520 nonbonded pdb=" NZ LYS H 108 " pdb=" OE2 GLU H 109 " model vdw 2.358 2.520 ... (remaining 41638 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 'G' selection = chain 'H' } ncs_group { reference = (chain 'N' and (resid 41 through 50 or resid 52 through 61)) selection = (chain 'T' and (resid 28 through 37 or resid 39 through 48)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.820 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.970 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.005 0.051 5626 Z= 0.295 Angle : 0.651 8.156 7813 Z= 0.387 Chirality : 0.043 0.156 854 Planarity : 0.005 0.062 832 Dihedral : 19.841 157.382 2168 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.32), residues: 532 helix: -1.71 (0.29), residues: 216 sheet: -0.87 (0.48), residues: 104 loop : -1.99 (0.38), residues: 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.606 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2732 time to fit residues: 21.6381 Evaluate side-chains 46 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.496 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 0.0070 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 22 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 178 ASN G 233 ASN H 3 GLN H 33 ASN H 101 HIS H 188 ASN H 233 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5626 Z= 0.178 Angle : 0.517 6.641 7813 Z= 0.300 Chirality : 0.039 0.145 854 Planarity : 0.004 0.053 832 Dihedral : 21.605 156.749 1054 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.22 % Allowed : 9.59 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.35), residues: 532 helix: -0.42 (0.34), residues: 212 sheet: -0.51 (0.52), residues: 98 loop : -1.54 (0.39), residues: 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.531 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.1671 time to fit residues: 11.9965 Evaluate side-chains 46 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0586 time to fit residues: 1.1203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 HIS G 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5626 Z= 0.190 Angle : 0.516 6.355 7813 Z= 0.298 Chirality : 0.039 0.146 854 Planarity : 0.004 0.049 832 Dihedral : 21.611 157.229 1054 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.22 % Allowed : 11.43 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.36), residues: 532 helix: 0.09 (0.35), residues: 212 sheet: -0.26 (0.53), residues: 98 loop : -1.41 (0.40), residues: 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.569 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 50 average time/residue: 0.1849 time to fit residues: 12.2014 Evaluate side-chains 48 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.565 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0506 time to fit residues: 0.9154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5626 Z= 0.212 Angle : 0.524 6.202 7813 Z= 0.301 Chirality : 0.039 0.146 854 Planarity : 0.004 0.046 832 Dihedral : 21.636 157.362 1054 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.22 % Allowed : 13.06 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.35), residues: 532 helix: 0.10 (0.35), residues: 218 sheet: -0.03 (0.60), residues: 80 loop : -1.63 (0.37), residues: 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.578 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.1885 time to fit residues: 12.7438 Evaluate side-chains 50 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.585 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0626 time to fit residues: 1.1759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5626 Z= 0.244 Angle : 0.556 11.383 7813 Z= 0.314 Chirality : 0.040 0.147 854 Planarity : 0.004 0.044 832 Dihedral : 21.683 157.585 1054 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.02 % Allowed : 14.29 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.35), residues: 532 helix: 0.16 (0.35), residues: 220 sheet: 0.04 (0.61), residues: 80 loop : -1.63 (0.38), residues: 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.584 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 0.1825 time to fit residues: 12.3345 Evaluate side-chains 47 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0495 time to fit residues: 0.9532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5626 Z= 0.211 Angle : 0.538 11.595 7813 Z= 0.304 Chirality : 0.039 0.146 854 Planarity : 0.004 0.043 832 Dihedral : 21.627 157.614 1054 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.02 % Allowed : 15.51 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.36), residues: 532 helix: 0.29 (0.35), residues: 220 sheet: 0.07 (0.61), residues: 80 loop : -1.60 (0.38), residues: 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.602 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.1915 time to fit residues: 12.4349 Evaluate side-chains 47 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0521 time to fit residues: 0.9405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 36 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5626 Z= 0.206 Angle : 0.540 10.900 7813 Z= 0.305 Chirality : 0.039 0.145 854 Planarity : 0.004 0.044 832 Dihedral : 21.621 157.709 1054 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.41 % Allowed : 16.73 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.36), residues: 532 helix: 0.43 (0.35), residues: 220 sheet: 0.12 (0.61), residues: 80 loop : -1.54 (0.38), residues: 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.589 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.1972 time to fit residues: 12.0003 Evaluate side-chains 47 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0748 time to fit residues: 0.8934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5626 Z= 0.219 Angle : 0.544 11.622 7813 Z= 0.307 Chirality : 0.039 0.145 854 Planarity : 0.004 0.047 832 Dihedral : 21.651 157.824 1054 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.41 % Allowed : 17.55 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.36), residues: 532 helix: 0.51 (0.35), residues: 220 sheet: 0.15 (0.61), residues: 80 loop : -1.52 (0.38), residues: 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.607 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.1965 time to fit residues: 12.1622 Evaluate side-chains 48 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.570 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0684 time to fit residues: 0.9797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 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 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5626 Z= 0.210 Angle : 0.537 11.340 7813 Z= 0.303 Chirality : 0.039 0.145 854 Planarity : 0.004 0.043 832 Dihedral : 21.640 157.785 1054 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.20 % Allowed : 17.35 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.36), residues: 532 helix: 0.59 (0.35), residues: 220 sheet: 0.16 (0.61), residues: 80 loop : -1.50 (0.38), residues: 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.631 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.2290 time to fit residues: 13.9724 Evaluate side-chains 47 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0588 time to fit residues: 0.9274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5626 Z= 0.186 Angle : 0.529 10.942 7813 Z= 0.298 Chirality : 0.039 0.144 854 Planarity : 0.004 0.043 832 Dihedral : 21.590 157.757 1054 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.20 % Allowed : 17.35 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.36), residues: 532 helix: 0.72 (0.36), residues: 220 sheet: 0.22 (0.61), residues: 80 loop : -1.46 (0.38), residues: 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.599 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.1952 time to fit residues: 12.3199 Evaluate side-chains 45 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.550 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.0050 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.132118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.112199 restraints weight = 5703.868| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.41 r_work: 0.3424 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5626 Z= 0.146 Angle : 0.514 11.059 7813 Z= 0.290 Chirality : 0.038 0.141 854 Planarity : 0.004 0.053 832 Dihedral : 21.532 158.195 1054 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 17.76 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.37), residues: 532 helix: 0.89 (0.36), residues: 220 sheet: 0.31 (0.62), residues: 80 loop : -1.38 (0.38), residues: 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1426.49 seconds wall clock time: 26 minutes 24.90 seconds (1584.90 seconds total)