Starting phenix.real_space_refine on Fri Mar 15 21:35:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/03_2024/7p0z_13153.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/03_2024/7p0z_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_13153/03_2024/7p0z_13153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/03_2024/7p0z_13153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/03_2024/7p0z_13153.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/03_2024/7p0z_13153.pdb" } resolution = 2.43 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= 0.246 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.71, per 1000 atoms: 0.52 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: 4.45 Conformation dependent library (CDL) restraints added in 2.1 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: 0.94 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: 3.28 Time building geometry restraints manager: 4.85 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: 0.810 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: 4.000 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 34.160 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.880 ------------------------------------------------------------------------------- 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 % Allowed : 0.00 % Favored : 100.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP D 156 HIS 0.009 0.004 HIS A 223 PHE 0.027 0.004 PHE D 159 TYR 0.028 0.006 TYR F 81 ARG 0.012 0.002 ARG A 165 *********************** 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 : 1.221 Fit side-chains revert: symmetry clash REVERT: A 221 ARG cc_start: 0.7647 (ptt-90) cc_final: 0.7442 (ptp90) REVERT: F 133 LEU cc_start: 0.8963 (mm) cc_final: 0.8714 (mt) REVERT: F 201 LEU cc_start: 0.9089 (mt) cc_final: 0.8878 (mt) REVERT: G 68 GLN cc_start: 0.8396 (mt0) cc_final: 0.8180 (mt0) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 1.4783 time to fit residues: 632.0697 Evaluate side-chains 256 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.0786 ------------------------------------------------------------------------------- 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: 0.8376 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13111 Z= 0.216 Angle : 0.530 7.474 17815 Z= 0.276 Chirality : 0.034 0.122 1967 Planarity : 0.004 0.033 2401 Dihedral : 3.712 13.699 1764 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.12 % Allowed : 14.21 % Favored : 82.66 % 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: 3.71 (0.20), residues: 1624 helix: 3.04 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 0.70 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 156 HIS 0.003 0.001 HIS G 223 PHE 0.015 0.002 PHE E 152 TYR 0.016 0.002 TYR G 59 ARG 0.006 0.000 ARG D 67 *********************** 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: 42 poor density : 296 time to evaluate : 1.614 Fit side-chains REVERT: C 257 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6609 (mt-10) REVERT: D 221 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7499 (ptp90) REVERT: F 133 LEU cc_start: 0.8858 (mm) cc_final: 0.8632 (mt) REVERT: F 201 LEU cc_start: 0.9036 (mt) cc_final: 0.8822 (mt) REVERT: G 66 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7450 (tp30) outliers start: 42 outliers final: 13 residues processed: 315 average time/residue: 1.1862 time to fit residues: 406.6572 Evaluate side-chains 295 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 281 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 188 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.0980 chunk 121 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 117 optimal weight: 0.0670 overall best weight: 1.4324 ------------------------------------------------------------------------------- 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: 0.8369 moved from start: 0.2055 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= 0.212 Angle : 0.482 5.762 17815 Z= 0.252 Chirality : 0.033 0.122 1967 Planarity : 0.004 0.031 2401 Dihedral : 3.465 12.952 1764 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 3.50 % Allowed : 15.70 % Favored : 80.80 % 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: 4.49 (0.20), residues: 1624 helix: 3.58 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.07 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 156 HIS 0.004 0.002 HIS B 223 PHE 0.016 0.002 PHE G 152 TYR 0.014 0.002 TYR C 59 ARG 0.004 0.000 ARG D 67 *********************** 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 336 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 289 time to evaluate : 2.094 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6911 (mt-10) REVERT: C 134 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8168 (mttt) REVERT: C 141 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: C 221 ARG cc_start: 0.7669 (ptp90) cc_final: 0.7283 (ptp90) REVERT: F 133 LEU cc_start: 0.8854 (mm) cc_final: 0.8608 (mt) REVERT: F 141 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: F 201 LEU cc_start: 0.9040 (mt) cc_final: 0.8818 (mt) REVERT: G 66 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7436 (tp30) REVERT: G 134 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8539 (mmtp) REVERT: G 193 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7542 (mp0) outliers start: 47 outliers final: 23 residues processed: 310 average time/residue: 1.0910 time to fit residues: 371.0409 Evaluate side-chains 310 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 281 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 259 VAL 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: 3.9990 chunk 76 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 41 optimal weight: 0.0010 chunk 129 optimal weight: 5.9990 overall best weight: 1.9390 ------------------------------------------------------------------------------- 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** F 253 GLN G 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2136 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= 0.254 Angle : 0.503 5.615 17815 Z= 0.262 Chirality : 0.035 0.123 1967 Planarity : 0.004 0.032 2401 Dihedral : 3.456 13.108 1764 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.87 % Allowed : 16.07 % Favored : 80.06 % 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: 4.70 (0.20), residues: 1624 helix: 3.71 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.26 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 156 HIS 0.005 0.002 HIS G 223 PHE 0.017 0.002 PHE G 152 TYR 0.013 0.002 TYR B 263 ARG 0.003 0.000 ARG D 67 *********************** 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 328 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 276 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6889 (mt-10) REVERT: C 134 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8193 (mttt) REVERT: C 141 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: C 221 ARG cc_start: 0.7619 (ptp90) cc_final: 0.7222 (ptp90) REVERT: D 221 ARG cc_start: 0.7656 (ptp90) cc_final: 0.7402 (ptp90) REVERT: F 141 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7002 (mt-10) REVERT: F 201 LEU cc_start: 0.9052 (mt) cc_final: 0.8811 (mt) REVERT: G 66 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7441 (tp30) REVERT: G 134 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8538 (mmtp) REVERT: G 189 ASP cc_start: 0.7825 (t70) cc_final: 0.7618 (t70) REVERT: G 193 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7544 (mp0) outliers start: 52 outliers final: 25 residues processed: 303 average time/residue: 1.1167 time to fit residues: 370.7439 Evaluate side-chains 297 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 266 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 276 LYS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 276 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 64 optimal weight: 0.0870 chunk 132 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 253 GLN G 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13111 Z= 0.182 Angle : 0.459 5.113 17815 Z= 0.239 Chirality : 0.032 0.119 1967 Planarity : 0.003 0.031 2401 Dihedral : 3.298 12.315 1764 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.35 % Allowed : 17.56 % Favored : 79.09 % 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: 5.04 (0.20), residues: 1624 helix: 3.96 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.35 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 156 HIS 0.003 0.001 HIS B 223 PHE 0.017 0.002 PHE G 152 TYR 0.011 0.002 TYR C 59 ARG 0.003 0.000 ARG D 67 *********************** 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 323 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 278 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6851 (mt-10) REVERT: C 134 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8203 (mttt) REVERT: C 141 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6926 (mt-10) REVERT: F 141 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7030 (mt-10) REVERT: F 201 LEU cc_start: 0.9034 (mt) cc_final: 0.8795 (mt) REVERT: G 66 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7429 (tp30) REVERT: G 134 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8533 (mmtp) outliers start: 45 outliers final: 24 residues processed: 303 average time/residue: 1.1250 time to fit residues: 373.3468 Evaluate side-chains 305 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 276 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 221 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13111 Z= 0.248 Angle : 0.495 4.776 17815 Z= 0.258 Chirality : 0.034 0.123 1967 Planarity : 0.004 0.032 2401 Dihedral : 3.362 12.861 1764 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.35 % Allowed : 18.82 % Favored : 77.83 % 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: 4.92 (0.20), residues: 1624 helix: 3.87 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.33 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 156 HIS 0.005 0.002 HIS B 223 PHE 0.017 0.002 PHE G 152 TYR 0.013 0.002 TYR G 59 ARG 0.003 0.000 ARG D 67 *********************** 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 324 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 279 time to evaluate : 1.610 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6854 (mt-10) REVERT: A 160 ASN cc_start: 0.9196 (OUTLIER) cc_final: 0.8843 (t0) REVERT: C 134 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8155 (mttt) REVERT: C 141 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6920 (mt-10) REVERT: F 141 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: F 201 LEU cc_start: 0.9047 (mt) cc_final: 0.8812 (mt) REVERT: G 66 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7451 (tp30) outliers start: 45 outliers final: 26 residues processed: 305 average time/residue: 1.1003 time to fit residues: 366.9904 Evaluate side-chains 306 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 275 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 276 LYS Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 276 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 94 optimal weight: 0.1980 chunk 71 optimal weight: 0.0570 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2504 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= 0.167 Angle : 0.455 5.900 17815 Z= 0.236 Chirality : 0.032 0.125 1967 Planarity : 0.003 0.035 2401 Dihedral : 3.218 13.328 1764 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 3.35 % Allowed : 19.27 % Favored : 77.38 % 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: 5.21 (0.20), residues: 1624 helix: 4.09 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.41 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 156 HIS 0.003 0.001 HIS B 223 PHE 0.017 0.002 PHE G 152 TYR 0.011 0.001 TYR C 59 ARG 0.015 0.000 ARG E 234 *********************** 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 338 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 293 time to evaluate : 1.577 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6798 (mt-10) REVERT: C 134 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8176 (mttt) REVERT: C 141 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6904 (mt-10) REVERT: C 226 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8167 (tt) REVERT: F 141 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7029 (mt-10) REVERT: F 201 LEU cc_start: 0.9022 (mt) cc_final: 0.8768 (mt) REVERT: G 66 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7441 (tp30) outliers start: 45 outliers final: 20 residues processed: 316 average time/residue: 1.1220 time to fit residues: 387.7369 Evaluate side-chains 300 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 275 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 276 LYS 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: 5.9990 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 13111 Z= 0.428 Angle : 0.600 6.263 17815 Z= 0.311 Chirality : 0.040 0.122 1967 Planarity : 0.005 0.037 2401 Dihedral : 3.623 13.914 1764 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.72 % Allowed : 19.27 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.46 (0.20), residues: 1624 helix: 3.50 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.28 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 156 HIS 0.007 0.003 HIS B 223 PHE 0.022 0.003 PHE A 159 TYR 0.018 0.003 TYR E 81 ARG 0.007 0.001 ARG E 234 *********************** 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 319 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 269 time to evaluate : 1.606 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6870 (mt-10) REVERT: A 160 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.8882 (t0) REVERT: C 134 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8127 (mttt) REVERT: C 141 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6942 (mt-10) REVERT: C 226 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8125 (tt) REVERT: F 141 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7118 (mt-10) REVERT: F 201 LEU cc_start: 0.9075 (mt) cc_final: 0.8838 (mt) REVERT: G 262 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7778 (tt0) outliers start: 50 outliers final: 30 residues processed: 303 average time/residue: 1.1323 time to fit residues: 376.6351 Evaluate side-chains 301 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 264 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 276 LYS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain G residue 276 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 94 optimal weight: 0.0370 chunk 152 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- 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: 0.8362 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13111 Z= 0.194 Angle : 0.476 5.174 17815 Z= 0.248 Chirality : 0.033 0.119 1967 Planarity : 0.004 0.037 2401 Dihedral : 3.326 13.856 1764 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.31 % Allowed : 20.83 % Favored : 76.86 % 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: 4.96 (0.20), residues: 1624 helix: 3.89 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.36 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 156 HIS 0.003 0.001 HIS B 223 PHE 0.017 0.002 PHE G 152 TYR 0.011 0.002 TYR C 59 ARG 0.007 0.000 ARG E 234 *********************** 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: 31 poor density : 272 time to evaluate : 1.438 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6756 (mt-10) REVERT: A 160 ASN cc_start: 0.9146 (OUTLIER) cc_final: 0.8787 (t0) REVERT: C 134 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8145 (mttt) REVERT: C 141 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6880 (mt-10) REVERT: D 262 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: F 141 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7028 (mt-10) REVERT: F 201 LEU cc_start: 0.9032 (mt) cc_final: 0.8783 (mt) REVERT: G 66 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7426 (tp30) REVERT: G 262 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7700 (tt0) outliers start: 31 outliers final: 15 residues processed: 290 average time/residue: 1.0681 time to fit residues: 340.5073 Evaluate side-chains 290 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 268 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 262 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.8370 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13111 Z= 0.227 Angle : 0.498 6.615 17815 Z= 0.257 Chirality : 0.034 0.148 1967 Planarity : 0.004 0.039 2401 Dihedral : 3.356 14.852 1764 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.53 % Allowed : 21.28 % Favored : 76.19 % 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: 4.95 (0.20), residues: 1624 helix: 3.88 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.38 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 156 HIS 0.004 0.002 HIS B 223 PHE 0.017 0.002 PHE G 152 TYR 0.012 0.002 TYR G 59 ARG 0.008 0.000 ARG E 234 ********************** 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 308 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 274 time to evaluate : 1.548 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6782 (mt-10) REVERT: A 160 ASN cc_start: 0.9180 (OUTLIER) cc_final: 0.8848 (t0) REVERT: C 134 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8157 (mttt) REVERT: C 141 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6906 (mt-10) REVERT: C 226 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8147 (tt) REVERT: F 141 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: F 201 LEU cc_start: 0.9040 (mt) cc_final: 0.8787 (mt) REVERT: G 66 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7426 (tp30) outliers start: 34 outliers final: 20 residues processed: 294 average time/residue: 1.0708 time to fit residues: 345.6831 Evaluate side-chains 298 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 272 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 276 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN D 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.092530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.085521 restraints weight = 20765.543| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.14 r_work: 0.3093 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13111 Z= 0.188 Angle : 0.478 6.721 17815 Z= 0.246 Chirality : 0.033 0.150 1967 Planarity : 0.004 0.042 2401 Dihedral : 3.269 14.633 1764 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.23 % Allowed : 21.50 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.12 (0.20), residues: 1624 helix: 4.00 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.44 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 156 HIS 0.003 0.001 HIS B 223 PHE 0.017 0.002 PHE G 152 TYR 0.011 0.002 TYR B 263 ARG 0.007 0.000 ARG E 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5721.13 seconds wall clock time: 101 minutes 4.26 seconds (6064.26 seconds total)