Starting phenix.real_space_refine on Sun Mar 17 02:20:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njv_12424/03_2024/7njv_12424_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njv_12424/03_2024/7njv_12424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njv_12424/03_2024/7njv_12424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njv_12424/03_2024/7njv_12424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njv_12424/03_2024/7njv_12424_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njv_12424/03_2024/7njv_12424_trim.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 1 7.06 5 S 28 5.16 5 C 5378 2.51 5 N 1318 2.21 5 O 1401 1.98 5 H 8337 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 65": "OE1" <-> "OE2" Residue "M GLU 48": "OE1" <-> "OE2" Residue "M PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 65": "OE1" <-> "OE2" Residue "N ASP 32": "OD1" <-> "OD2" Residue "R GLU 65": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16463 Number of models: 1 Model: "" Number of chains: 13 Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 979 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "d" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 952 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "N" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C06 BQ1 N 101 " occ=0.75 ... (35 atoms not shown) pdb="BR BQ1 N 101 " occ=0.75 Time building chain proxies: 7.54, per 1000 atoms: 0.46 Number of scatterers: 16463 At special positions: 0 Unit cell: (94.62, 77.19, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 1 34.99 S 28 16.00 O 1401 8.00 N 1318 7.00 C 5378 6.00 H 8337 1.00 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: 13.61 Conformation dependent library (CDL) restraints added in 2.1 seconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 2 sheets defined 88.0% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'L' and resid 4 through 46 removed outlier: 3.645A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 81 removed outlier: 4.398A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.049A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 removed outlier: 3.671A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 51 removed outlier: 4.393A pdb=" N GLY M 51 " --> pdb=" O GLU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 80 removed outlier: 3.632A pdb=" N LEU M 63 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 Processing helix chain 'N' and resid 49 through 80 removed outlier: 4.047A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.576A pdb=" N ALA N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 removed outlier: 3.679A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 80 removed outlier: 4.525A pdb=" N ARG O 52 " --> pdb=" O GLU O 48 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.572A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.731A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 50 removed outlier: 3.631A pdb=" N GLN P 50 " --> pdb=" O PRO P 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 47 through 50' Processing helix chain 'P' and resid 53 through 80 Processing helix chain 'Q' and resid 4 through 46 removed outlier: 3.743A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 80 removed outlier: 4.497A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix Processing helix chain 'R' and resid 4 through 46 Processing helix chain 'R' and resid 49 through 81 removed outlier: 4.780A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix Processing helix chain 'S' and resid 4 through 46 Processing helix chain 'S' and resid 49 through 81 removed outlier: 4.543A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.971A pdb=" N ALA S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.744A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 80 removed outlier: 3.604A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.859A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 53 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.541A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.558A pdb=" N ILE a 160 " --> pdb=" O VAL a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 204 Proline residue: a 182 - end of helix removed outlier: 3.858A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 3.966A pdb=" N TRP a 212 " --> pdb=" O TRP a 208 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.906A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 49 removed outlier: 3.510A pdb=" N ALA b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 84 Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 61 Processing sheet with id=AA1, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'a' and resid 112 through 114 800 hydrogen bonds defined for protein. 2388 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: 7.43 Time building geometry restraints manager: 14.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 8336 1.06 - 1.28: 1310 1.28 - 1.50: 3497 1.50 - 1.72: 3436 1.72 - 1.94: 56 Bond restraints: 16635 Sorted by residual: bond pdb=" C17 BQ1 N 101 " pdb=" O03 BQ1 N 101 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C17 BQ1 N 101 " pdb=" N05 BQ1 N 101 " ideal model delta sigma weight residual 1.297 1.354 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" C35 BQ1 N 101 " pdb="BR BQ1 N 101 " ideal model delta sigma weight residual 1.888 1.941 -0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" C13 BQ1 N 101 " pdb=" C16 BQ1 N 101 " ideal model delta sigma weight residual 1.426 1.375 0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" C10 BQ1 N 101 " pdb=" C17 BQ1 N 101 " ideal model delta sigma weight residual 1.437 1.392 0.045 2.00e-02 2.50e+03 5.09e+00 ... (remaining 16630 not shown) Histogram of bond angle deviations from ideal: 99.77 - 107.56: 751 107.56 - 115.35: 20623 115.35 - 123.14: 7526 123.14 - 130.93: 1257 130.93 - 138.72: 18 Bond angle restraints: 30175 Sorted by residual: angle pdb=" C10 BQ1 N 101 " pdb=" C17 BQ1 N 101 " pdb=" O03 BQ1 N 101 " ideal model delta sigma weight residual 115.66 138.72 -23.06 3.00e+00 1.11e-01 5.91e+01 angle pdb=" N05 BQ1 N 101 " pdb=" C17 BQ1 N 101 " pdb=" O03 BQ1 N 101 " ideal model delta sigma weight residual 119.50 101.21 18.29 3.00e+00 1.11e-01 3.72e+01 angle pdb=" C06 BQ1 N 101 " pdb=" C09 BQ1 N 101 " pdb=" C14 BQ1 N 101 " ideal model delta sigma weight residual 118.36 106.61 11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C07 BQ1 N 101 " pdb=" C10 BQ1 N 101 " pdb=" C17 BQ1 N 101 " ideal model delta sigma weight residual 118.88 108.06 10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" C06 BQ1 N 101 " pdb=" C09 BQ1 N 101 " pdb=" C13 BQ1 N 101 " ideal model delta sigma weight residual 123.57 134.30 -10.73 3.00e+00 1.11e-01 1.28e+01 ... (remaining 30170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 6704 16.78 - 33.56: 668 33.56 - 50.34: 175 50.34 - 67.12: 232 67.12 - 83.90: 7 Dihedral angle restraints: 7786 sinusoidal: 4177 harmonic: 3609 Sorted by residual: dihedral pdb=" CA GLN L 46 " pdb=" C GLN L 46 " pdb=" N PRO L 47 " pdb=" CA PRO L 47 " ideal model delta harmonic sigma weight residual -180.00 -164.08 -15.92 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA PHE P 78 " pdb=" C PHE P 78 " pdb=" N VAL P 79 " pdb=" CA VAL P 79 " ideal model delta harmonic sigma weight residual -180.00 -164.42 -15.58 0 5.00e+00 4.00e-02 9.71e+00 dihedral pdb=" CB MET d 1 " pdb=" CG MET d 1 " pdb=" SD MET d 1 " pdb=" CE MET d 1 " ideal model delta sinusoidal sigma weight residual -180.00 -121.65 -58.35 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 7783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1178 0.068 - 0.136: 145 0.136 - 0.204: 0 0.204 - 0.273: 0 0.273 - 0.341: 1 Chirality restraints: 1324 Sorted by residual: chirality pdb=" C07 BQ1 N 101 " pdb=" C06 BQ1 N 101 " pdb=" C10 BQ1 N 101 " pdb=" C12 BQ1 N 101 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA ILE b 26 " pdb=" N ILE b 26 " pdb=" C ILE b 26 " pdb=" CB ILE b 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA PRO L 47 " pdb=" N PRO L 47 " pdb=" C PRO L 47 " pdb=" CB PRO L 47 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 1321 not shown) Planarity restraints: 2498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA a 86 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO a 87 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO a 87 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO a 87 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA d 42 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C ALA d 42 " -0.028 2.00e-02 2.50e+03 pdb=" O ALA d 42 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU d 43 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 64 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C VAL P 64 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL P 64 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU P 65 " 0.009 2.00e-02 2.50e+03 ... (remaining 2495 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.24: 1508 2.24 - 2.85: 39759 2.85 - 3.47: 50139 3.47 - 4.08: 70642 4.08 - 4.70: 112069 Nonbonded interactions: 274117 Sorted by model distance: nonbonded pdb=" OD1 ASN a 132 " pdb=" H ASN b 28 " model vdw 1.625 1.850 nonbonded pdb=" O ASN S 6 " pdb=" HG1 THR S 10 " model vdw 1.681 1.850 nonbonded pdb="HE22 GLN b 77 " pdb=" OD1 ASP d 55 " model vdw 1.686 1.850 nonbonded pdb=" HG SER a 55 " pdb=" OE1 GLU b 59 " model vdw 1.688 1.850 nonbonded pdb=" O ASN R 6 " pdb=" HG1 THR R 10 " model vdw 1.702 1.850 ... (remaining 274112 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 'L' selection = chain 'M' selection = (chain 'N' and resid 3 through 86) selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 6.660 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: 0.280 Extract box with map and model: 25.060 Check model and map are aligned: 0.280 Set scattering table: 0.150 Process input model: 58.700 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 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 : 0.003 0.069 8298 Z= 0.196 Angle : 0.604 23.064 11277 Z= 0.288 Chirality : 0.039 0.341 1324 Planarity : 0.005 0.044 1443 Dihedral : 13.575 83.904 2816 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 2.26 (0.27), residues: 1094 helix: 1.55 (0.18), residues: 943 sheet: None (None), residues: 0 loop : 1.67 (0.60), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.012 0.001 PHE S 74 TYR 0.023 0.001 TYR a 145 ARG 0.002 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: a 73 MET cc_start: 0.8879 (mmt) cc_final: 0.8643 (mmt) REVERT: a 192 ASN cc_start: 0.8283 (t0) cc_final: 0.8082 (t0) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 2.6343 time to fit residues: 308.5909 Evaluate side-chains 72 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 71 ASN a 192 ASN d 33 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8298 Z= 0.305 Angle : 0.522 5.393 11277 Z= 0.287 Chirality : 0.039 0.132 1324 Planarity : 0.004 0.038 1443 Dihedral : 5.550 59.964 1176 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.07 % Allowed : 7.25 % Favored : 90.67 % 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: 3.45 (0.25), residues: 1094 helix: 2.43 (0.16), residues: 944 sheet: None (None), residues: 0 loop : 1.43 (0.57), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.004 0.001 HIS a 146 PHE 0.017 0.002 PHE S 74 TYR 0.022 0.001 TYR a 145 ARG 0.005 0.000 ARG T 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: Q 65 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: a 73 MET cc_start: 0.9062 (mmt) cc_final: 0.8603 (mmt) outliers start: 16 outliers final: 7 residues processed: 83 average time/residue: 2.6141 time to fit residues: 231.4243 Evaluate side-chains 79 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain Q residue 65 GLU Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 239 LEU Chi-restraints excluded: chain d residue 57 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 97 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.0670 chunk 96 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 0.0980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 71 ASN d 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8298 Z= 0.188 Angle : 0.468 5.197 11277 Z= 0.254 Chirality : 0.038 0.127 1324 Planarity : 0.004 0.037 1443 Dihedral : 4.931 32.644 1176 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.46 % Allowed : 7.25 % Favored : 90.28 % 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: 4.03 (0.25), residues: 1094 helix: 2.85 (0.16), residues: 944 sheet: None (None), residues: 0 loop : 1.45 (0.57), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.013 0.001 PHE M 69 TYR 0.020 0.001 TYR a 145 ARG 0.003 0.000 ARG T 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 73 MET cc_start: 0.9100 (mmt) cc_final: 0.8661 (mmt) outliers start: 19 outliers final: 5 residues processed: 87 average time/residue: 2.4508 time to fit residues: 228.2362 Evaluate side-chains 76 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 239 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 192 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8298 Z= 0.288 Angle : 0.497 5.350 11277 Z= 0.270 Chirality : 0.039 0.126 1324 Planarity : 0.004 0.037 1443 Dihedral : 4.938 32.019 1176 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.33 % Allowed : 7.51 % Favored : 90.16 % 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: 3.99 (0.25), residues: 1094 helix: 2.84 (0.17), residues: 944 sheet: None (None), residues: 0 loop : 1.27 (0.56), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.004 0.001 HIS a 146 PHE 0.015 0.002 PHE S 74 TYR 0.020 0.001 TYR a 145 ARG 0.002 0.000 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: a 73 MET cc_start: 0.9139 (mmt) cc_final: 0.8638 (mmt) REVERT: d 46 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6354 (mt-10) outliers start: 18 outliers final: 7 residues processed: 82 average time/residue: 2.7172 time to fit residues: 237.2768 Evaluate side-chains 76 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain R residue 21 MET Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 239 LEU Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 57 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 192 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8298 Z= 0.238 Angle : 0.480 5.295 11277 Z= 0.260 Chirality : 0.038 0.126 1324 Planarity : 0.004 0.038 1443 Dihedral : 4.823 31.639 1176 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.33 % Allowed : 7.90 % Favored : 89.77 % 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: 4.07 (0.26), residues: 1094 helix: 2.90 (0.17), residues: 944 sheet: None (None), residues: 0 loop : 1.30 (0.57), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.014 0.001 PHE N 74 TYR 0.019 0.001 TYR a 145 ARG 0.002 0.000 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: a 73 MET cc_start: 0.9158 (mmt) cc_final: 0.8588 (mmt) REVERT: d 46 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6368 (mt-10) outliers start: 18 outliers final: 7 residues processed: 84 average time/residue: 2.5674 time to fit residues: 230.5544 Evaluate side-chains 76 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 239 LEU Chi-restraints excluded: chain b residue 46 SER Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 57 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8298 Z= 0.320 Angle : 0.510 5.357 11277 Z= 0.279 Chirality : 0.039 0.130 1324 Planarity : 0.004 0.039 1443 Dihedral : 4.966 32.234 1176 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.85 % Allowed : 8.16 % Favored : 88.99 % 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: 3.90 (0.25), residues: 1094 helix: 2.79 (0.17), residues: 944 sheet: None (None), residues: 0 loop : 1.15 (0.56), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.004 0.001 HIS a 146 PHE 0.016 0.002 PHE S 74 TYR 0.019 0.001 TYR a 145 ARG 0.002 0.000 ARG L 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 68 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 65 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: a 73 MET cc_start: 0.9166 (mmt) cc_final: 0.8539 (mmt) REVERT: a 205 MET cc_start: 0.8644 (mtt) cc_final: 0.8422 (mtt) REVERT: d 46 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6320 (mt-10) outliers start: 22 outliers final: 10 residues processed: 81 average time/residue: 2.7477 time to fit residues: 237.2376 Evaluate side-chains 77 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain Q residue 71 ASN Chi-restraints excluded: chain R residue 21 MET Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 239 LEU Chi-restraints excluded: chain b residue 46 SER Chi-restraints excluded: chain b residue 55 LYS Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 57 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 chunk 64 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8298 Z= 0.234 Angle : 0.483 5.256 11277 Z= 0.262 Chirality : 0.038 0.124 1324 Planarity : 0.004 0.038 1443 Dihedral : 4.885 32.422 1176 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.94 % Allowed : 9.84 % Favored : 88.21 % 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: 4.05 (0.26), residues: 1094 helix: 2.88 (0.17), residues: 944 sheet: None (None), residues: 0 loop : 1.24 (0.57), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.014 0.001 PHE N 74 TYR 0.019 0.001 TYR a 145 ARG 0.002 0.000 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 65 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: a 73 MET cc_start: 0.9175 (mmt) cc_final: 0.8582 (mmt) REVERT: d 46 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6289 (mt-10) outliers start: 15 outliers final: 8 residues processed: 76 average time/residue: 2.7183 time to fit residues: 220.1707 Evaluate side-chains 76 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain Q residue 71 ASN Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 239 LEU Chi-restraints excluded: chain b residue 46 SER Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 57 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 93 optimal weight: 0.1980 chunk 98 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 192 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8298 Z= 0.212 Angle : 0.474 5.238 11277 Z= 0.256 Chirality : 0.038 0.126 1324 Planarity : 0.004 0.038 1443 Dihedral : 4.807 32.432 1176 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.33 % Allowed : 9.33 % Favored : 88.34 % 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: 4.16 (0.26), residues: 1094 helix: 2.95 (0.17), residues: 944 sheet: None (None), residues: 0 loop : 1.31 (0.57), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.014 0.001 PHE N 74 TYR 0.019 0.001 TYR a 145 ARG 0.002 0.000 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 65 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: a 73 MET cc_start: 0.9168 (mmt) cc_final: 0.8600 (mmt) REVERT: d 46 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6294 (mt-10) outliers start: 18 outliers final: 9 residues processed: 82 average time/residue: 2.5624 time to fit residues: 224.4567 Evaluate side-chains 76 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain Q residue 71 ASN Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain a residue 239 LEU Chi-restraints excluded: chain b residue 46 SER Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 57 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 192 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8298 Z= 0.280 Angle : 0.496 5.303 11277 Z= 0.269 Chirality : 0.039 0.126 1324 Planarity : 0.004 0.039 1443 Dihedral : 4.888 32.496 1176 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.68 % Allowed : 10.23 % Favored : 88.08 % 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: 4.06 (0.25), residues: 1094 helix: 2.89 (0.17), residues: 944 sheet: None (None), residues: 0 loop : 1.26 (0.57), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.015 0.002 PHE S 74 TYR 0.019 0.001 TYR a 145 ARG 0.002 0.000 ARG L 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 65 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: a 73 MET cc_start: 0.9176 (mmt) cc_final: 0.8590 (mmt) REVERT: d 46 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6286 (mt-10) outliers start: 13 outliers final: 9 residues processed: 77 average time/residue: 2.7539 time to fit residues: 225.6513 Evaluate side-chains 75 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain Q residue 71 ASN Chi-restraints excluded: chain S residue 48 GLU Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 239 LEU Chi-restraints excluded: chain b residue 46 SER Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 57 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 0.0570 chunk 84 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 90 optimal weight: 0.4980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8298 Z= 0.206 Angle : 0.475 5.289 11277 Z= 0.257 Chirality : 0.038 0.126 1324 Planarity : 0.004 0.038 1443 Dihedral : 4.786 32.548 1176 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.68 % Allowed : 10.62 % Favored : 87.69 % 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: 4.24 (0.26), residues: 1094 helix: 3.00 (0.17), residues: 944 sheet: None (None), residues: 0 loop : 1.40 (0.58), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.013 0.001 PHE N 74 TYR 0.019 0.001 TYR a 145 ARG 0.002 0.000 ARG d 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 ARG cc_start: 0.5894 (tmt170) cc_final: 0.5300 (tpt170) REVERT: T 65 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: a 73 MET cc_start: 0.9175 (mmt) cc_final: 0.8617 (mmt) REVERT: d 46 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6266 (mt-10) outliers start: 13 outliers final: 9 residues processed: 74 average time/residue: 2.7272 time to fit residues: 214.9724 Evaluate side-chains 75 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain Q residue 71 ASN Chi-restraints excluded: chain S residue 48 GLU Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 239 LEU Chi-restraints excluded: chain b residue 46 SER Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 57 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.069550 restraints weight = 39654.793| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.56 r_work: 0.2762 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8298 Z= 0.273 Angle : 0.496 5.374 11277 Z= 0.270 Chirality : 0.039 0.125 1324 Planarity : 0.004 0.039 1443 Dihedral : 4.874 32.439 1176 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.42 % Allowed : 10.88 % Favored : 87.69 % 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: 4.13 (0.25), residues: 1094 helix: 2.93 (0.17), residues: 944 sheet: None (None), residues: 0 loop : 1.32 (0.57), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.015 0.002 PHE S 74 TYR 0.019 0.001 TYR a 145 ARG 0.002 0.000 ARG L 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5484.02 seconds wall clock time: 96 minutes 27.11 seconds (5787.11 seconds total)