Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 17:26:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/04_2023/7p0z_13153.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/04_2023/7p0z_13153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/04_2023/7p0z_13153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/04_2023/7p0z_13153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/04_2023/7p0z_13153.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/04_2023/7p0z_13153.pdb" } resolution = 2.43 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= 0.246 sd= 1.026 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8008 2.51 5 N 2247 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 66": "OE1" <-> "OE2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 66": "OE1" <-> "OE2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12873 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Chain: "F" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 7.17, per 1000 atoms: 0.56 Number of scatterers: 12873 At special positions: 0 Unit cell: (104.25, 103.416, 104.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2576 8.00 N 2247 7.00 C 8008 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: 5.72 Conformation dependent library (CDL) restraints added in 1.9 seconds 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 75.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.553A pdb=" N ILE A 14 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 80 Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 146 through 165 Processing helix chain 'A' and resid 166 through 171 removed outlier: 4.168A pdb=" N ARG A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 223 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 241 through 267 removed outlier: 4.461A pdb=" N LYS A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.553A pdb=" N ILE B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 80 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 146 through 165 Processing helix chain 'B' and resid 166 through 171 removed outlier: 4.168A pdb=" N ARG B 169 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 223 Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 241 through 267 removed outlier: 4.461A pdb=" N LYS B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.554A pdb=" N ILE C 14 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 80 Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 146 through 165 Processing helix chain 'C' and resid 166 through 171 removed outlier: 4.169A pdb=" N ARG C 169 " --> pdb=" O ASP C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 223 Processing helix chain 'C' and resid 225 through 236 Processing helix chain 'C' and resid 241 through 267 removed outlier: 4.461A pdb=" N LYS C 247 " --> pdb=" O GLU C 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.553A pdb=" N ILE D 14 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 80 Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 146 through 165 Processing helix chain 'D' and resid 166 through 171 removed outlier: 4.168A pdb=" N ARG D 169 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 223 Processing helix chain 'D' and resid 225 through 236 Processing helix chain 'D' and resid 241 through 267 removed outlier: 4.460A pdb=" N LYS D 247 " --> pdb=" O GLU D 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 22 removed outlier: 3.553A pdb=" N ILE E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 80 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 146 through 165 Processing helix chain 'E' and resid 166 through 171 removed outlier: 4.168A pdb=" N ARG E 169 " --> pdb=" O ASP E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 223 Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 241 through 267 removed outlier: 4.460A pdb=" N LYS E 247 " --> pdb=" O GLU E 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.553A pdb=" N ILE F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 80 Processing helix chain 'F' and resid 130 through 142 Processing helix chain 'F' and resid 146 through 165 Processing helix chain 'F' and resid 166 through 171 removed outlier: 4.169A pdb=" N ARG F 169 " --> pdb=" O ASP F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 223 Processing helix chain 'F' and resid 225 through 236 Processing helix chain 'F' and resid 241 through 267 removed outlier: 4.461A pdb=" N LYS F 247 " --> pdb=" O GLU F 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 22 removed outlier: 3.553A pdb=" N ILE G 14 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 80 Processing helix chain 'G' and resid 130 through 142 Processing helix chain 'G' and resid 146 through 165 Processing helix chain 'G' and resid 166 through 171 removed outlier: 4.169A pdb=" N ARG G 169 " --> pdb=" O ASP G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 223 Processing helix chain 'G' and resid 225 through 236 Processing helix chain 'G' and resid 241 through 267 removed outlier: 4.461A pdb=" N LYS G 247 " --> pdb=" O GLU G 243 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2982 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.75 Time building geometry restraints manager: 6.11 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: 4008 1.33 - 1.44: 1633 1.44 - 1.56: 7393 1.56 - 1.68: 0 1.68 - 1.80: 77 Bond restraints: 13111 Sorted by residual: bond pdb=" CB ARG F 220 " pdb=" CG ARG F 220 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.83e+00 bond pdb=" CB ARG C 220 " pdb=" CG ARG C 220 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.80e+00 bond pdb=" CB ARG G 220 " pdb=" CG ARG G 220 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.80e+00 bond pdb=" CB ARG E 220 " pdb=" CG ARG E 220 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.72e+00 bond pdb=" CB ARG B 220 " pdb=" CG ARG B 220 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.70e+00 ... (remaining 13106 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.35: 301 105.35 - 112.51: 7056 112.51 - 119.68: 4423 119.68 - 126.84: 5868 126.84 - 134.01: 167 Bond angle restraints: 17815 Sorted by residual: angle pdb=" C ASN C 264 " pdb=" N THR C 265 " pdb=" CA THR C 265 " ideal model delta sigma weight residual 120.58 114.74 5.84 1.71e+00 3.42e-01 1.17e+01 angle pdb=" C ASN F 264 " pdb=" N THR F 265 " pdb=" CA THR F 265 " ideal model delta sigma weight residual 120.58 114.74 5.84 1.71e+00 3.42e-01 1.17e+01 angle pdb=" C ASN D 264 " pdb=" N THR D 265 " pdb=" CA THR D 265 " ideal model delta sigma weight residual 120.58 114.76 5.82 1.71e+00 3.42e-01 1.16e+01 angle pdb=" C ASN B 264 " pdb=" N THR B 265 " pdb=" CA THR B 265 " ideal model delta sigma weight residual 120.58 114.77 5.81 1.71e+00 3.42e-01 1.16e+01 angle pdb=" C ASN E 264 " pdb=" N THR E 265 " pdb=" CA THR E 265 " ideal model delta sigma weight residual 120.58 114.78 5.80 1.71e+00 3.42e-01 1.15e+01 ... (remaining 17810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 7420 16.61 - 33.22: 539 33.22 - 49.83: 77 49.83 - 66.44: 35 66.44 - 83.06: 42 Dihedral angle restraints: 8113 sinusoidal: 3241 harmonic: 4872 Sorted by residual: dihedral pdb=" CB GLU A 270 " pdb=" CG GLU A 270 " pdb=" CD GLU A 270 " pdb=" OE1 GLU A 270 " ideal model delta sinusoidal sigma weight residual 0.00 -83.06 83.06 1 3.00e+01 1.11e-03 9.38e+00 dihedral pdb=" CB GLU C 270 " pdb=" CG GLU C 270 " pdb=" CD GLU C 270 " pdb=" OE1 GLU C 270 " ideal model delta sinusoidal sigma weight residual 0.00 -83.04 83.04 1 3.00e+01 1.11e-03 9.37e+00 dihedral pdb=" CB GLU E 270 " pdb=" CG GLU E 270 " pdb=" CD GLU E 270 " pdb=" OE1 GLU E 270 " ideal model delta sinusoidal sigma weight residual 0.00 -83.02 83.02 1 3.00e+01 1.11e-03 9.37e+00 ... (remaining 8110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 751 0.032 - 0.064: 644 0.064 - 0.097: 378 0.097 - 0.129: 159 0.129 - 0.161: 35 Chirality restraints: 1967 Sorted by residual: chirality pdb=" CA ASN C 273 " pdb=" N ASN C 273 " pdb=" C ASN C 273 " pdb=" CB ASN C 273 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA ASN E 273 " pdb=" N ASN E 273 " pdb=" C ASN E 273 " pdb=" CB ASN E 273 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ASN F 273 " pdb=" N ASN F 273 " pdb=" C ASN F 273 " pdb=" CB ASN F 273 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1964 not shown) Planarity restraints: 2401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 81 " -0.019 2.00e-02 2.50e+03 1.21e-02 2.94e+00 pdb=" CG TYR A 81 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 81 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 81 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 81 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 81 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 81 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 81 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 81 " -0.019 2.00e-02 2.50e+03 1.21e-02 2.93e+00 pdb=" CG TYR C 81 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 81 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 81 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 81 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 81 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 81 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 81 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 273 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" CG ASN A 273 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 273 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 273 " 0.010 2.00e-02 2.50e+03 ... (remaining 2398 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 604 2.69 - 3.24: 13166 3.24 - 3.80: 22991 3.80 - 4.35: 25703 4.35 - 4.90: 42627 Nonbonded interactions: 105091 Sorted by model distance: nonbonded pdb=" OE1 GLU C 257 " pdb=" NH1 ARG D 221 " model vdw 2.141 2.520 nonbonded pdb=" OE1 GLU E 257 " pdb=" NH1 ARG F 221 " model vdw 2.145 2.520 nonbonded pdb=" OE1 GLU B 257 " pdb=" NH1 ARG C 221 " model vdw 2.148 2.520 nonbonded pdb=" OE1 GLU D 257 " pdb=" NH1 ARG E 221 " model vdw 2.148 2.520 nonbonded pdb=" OE1 GLU A 257 " pdb=" NH1 ARG B 221 " model vdw 2.151 2.520 ... (remaining 105086 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.420 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 35.200 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.016 0.078 13111 Z= 1.025 Angle : 0.943 7.606 17815 Z= 0.523 Chirality : 0.059 0.161 1967 Planarity : 0.006 0.041 2401 Dihedral : 14.023 83.055 4921 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.20), residues: 1624 helix: 1.71 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 0.07 (0.30), residues: 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 1.583 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 1.4622 time to fit residues: 625.8131 Evaluate side-chains 256 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.548 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 253 GLN D 244 GLN E 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 13111 Z= 0.188 Angle : 0.510 8.867 17815 Z= 0.265 Chirality : 0.033 0.116 1967 Planarity : 0.003 0.032 2401 Dihedral : 3.620 13.359 1764 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.20), residues: 1624 helix: 3.18 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 0.73 (0.30), residues: 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 300 time to evaluate : 1.461 Fit side-chains outliers start: 38 outliers final: 9 residues processed: 319 average time/residue: 1.1941 time to fit residues: 414.6550 Evaluate side-chains 290 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 281 time to evaluate : 1.485 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 1 residues processed: 8 average time/residue: 0.2676 time to fit residues: 4.9553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 117 optimal weight: 0.0020 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 13111 Z= 0.287 Angle : 0.524 5.745 17815 Z= 0.274 Chirality : 0.035 0.124 1967 Planarity : 0.004 0.034 2401 Dihedral : 3.559 13.515 1764 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.30 (0.20), residues: 1624 helix: 3.45 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.00 (0.30), residues: 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 278 time to evaluate : 1.604 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 25 residues processed: 303 average time/residue: 1.1471 time to fit residues: 381.1169 Evaluate side-chains 296 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 271 time to evaluate : 1.651 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 12 residues processed: 13 average time/residue: 0.5028 time to fit residues: 10.0119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN C 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13111 Z= 0.198 Angle : 0.470 5.173 17815 Z= 0.245 Chirality : 0.033 0.120 1967 Planarity : 0.003 0.032 2401 Dihedral : 3.371 12.768 1764 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer Outliers : 3.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.84 (0.20), residues: 1624 helix: 3.82 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.25 (0.31), residues: 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 287 time to evaluate : 1.602 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 307 average time/residue: 1.1040 time to fit residues: 372.0713 Evaluate side-chains 298 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 276 time to evaluate : 1.449 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 12 residues processed: 10 average time/residue: 0.3307 time to fit residues: 6.3285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN F 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 13111 Z= 0.256 Angle : 0.504 5.492 17815 Z= 0.262 Chirality : 0.034 0.123 1967 Planarity : 0.004 0.032 2401 Dihedral : 3.414 13.089 1764 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer Outliers : 3.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.80 (0.20), residues: 1624 helix: 3.77 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.32 (0.31), residues: 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 273 time to evaluate : 1.608 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 25 residues processed: 300 average time/residue: 1.1413 time to fit residues: 375.0573 Evaluate side-chains 292 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 267 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 18 residues processed: 7 average time/residue: 0.1182 time to fit residues: 3.6119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 0.0670 chunk 30 optimal weight: 0.0000 chunk 91 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 150 optimal weight: 0.6980 overall best weight: 0.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN F 253 GLN G 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 13111 Z= 0.132 Angle : 0.422 4.117 17815 Z= 0.221 Chirality : 0.031 0.116 1967 Planarity : 0.003 0.030 2401 Dihedral : 3.074 10.536 1764 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.43 (0.21), residues: 1624 helix: 4.28 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.40 (0.33), residues: 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 312 time to evaluate : 1.764 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 13 residues processed: 333 average time/residue: 1.0596 time to fit residues: 388.5601 Evaluate side-chains 307 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 294 time to evaluate : 1.466 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1411 time to fit residues: 2.6631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 94 optimal weight: 0.0010 chunk 71 optimal weight: 0.0000 chunk 96 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13111 Z= 0.183 Angle : 0.454 5.781 17815 Z= 0.237 Chirality : 0.033 0.168 1967 Planarity : 0.003 0.031 2401 Dihedral : 3.123 11.158 1764 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.43 (0.20), residues: 1624 helix: 4.25 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.47 (0.32), residues: 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 291 time to evaluate : 1.623 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 311 average time/residue: 1.1105 time to fit residues: 378.6808 Evaluate side-chains 296 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 278 time to evaluate : 1.650 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1140 time to fit residues: 3.0130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN G 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 13111 Z= 0.336 Angle : 0.567 5.810 17815 Z= 0.293 Chirality : 0.037 0.127 1967 Planarity : 0.005 0.043 2401 Dihedral : 3.467 12.949 1764 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.85 (0.20), residues: 1624 helix: 3.80 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.35 (0.31), residues: 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 273 time to evaluate : 1.659 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 297 average time/residue: 1.0666 time to fit residues: 349.3396 Evaluate side-chains 293 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 270 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 6 average time/residue: 0.1373 time to fit residues: 3.4455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 94 optimal weight: 0.0470 chunk 152 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN F 197 HIS F 253 GLN G 264 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 13111 Z= 0.239 Angle : 0.508 6.670 17815 Z= 0.264 Chirality : 0.034 0.120 1967 Planarity : 0.004 0.036 2401 Dihedral : 3.366 12.653 1764 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.94 (0.20), residues: 1624 helix: 3.87 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.37 (0.32), residues: 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 274 time to evaluate : 1.585 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 296 average time/residue: 1.1158 time to fit residues: 362.8325 Evaluate side-chains 285 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 265 time to evaluate : 1.465 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.9544 time to fit residues: 4.1562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 147 optimal weight: 0.0060 chunk 127 optimal weight: 0.0670 chunk 13 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.9936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 13111 Z= 0.176 Angle : 0.476 6.244 17815 Z= 0.246 Chirality : 0.033 0.145 1967 Planarity : 0.004 0.041 2401 Dihedral : 3.237 14.070 1764 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.22 (0.20), residues: 1624 helix: 4.08 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.44 (0.32), residues: 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 291 time to evaluate : 1.519 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 17 residues processed: 308 average time/residue: 1.1045 time to fit residues: 373.9369 Evaluate side-chains 298 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 281 time to evaluate : 1.539 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.1656 time to fit residues: 2.6640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 0.0370 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 127 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 chunk 92 optimal weight: 10.0000 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN F 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.093790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.086940 restraints weight = 20951.094| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.15 r_work: 0.3128 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 13111 Z= 0.147 Angle : 0.453 6.752 17815 Z= 0.233 Chirality : 0.032 0.144 1967 Planarity : 0.004 0.045 2401 Dihedral : 3.107 14.349 1764 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.47 (0.20), residues: 1624 helix: 4.27 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.53 (0.33), residues: 420 =============================================================================== Job complete usr+sys time: 5789.46 seconds wall clock time: 102 minutes 46.93 seconds (6166.93 seconds total)