Starting phenix.real_space_refine (version: dev) on Sat Feb 18 04:59:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/02_2023/6u5h_20646.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/02_2023/6u5h_20646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/02_2023/6u5h_20646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/02_2023/6u5h_20646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/02_2023/6u5h_20646.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/02_2023/6u5h_20646.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7326 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2442 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2442 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2442 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.62, per 1000 atoms: 0.63 Number of scatterers: 7326 At special positions: 0 Unit cell: (90.567, 94.731, 78.075, 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 1392 8.00 N 1362 7.00 C 4530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.2 seconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 10.1% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 155 through 160 removed outlier: 3.754A pdb=" N ASP C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.661A pdb=" N GLN C 176 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER C 177 " --> pdb=" O PRO C 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 173 through 177' Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.609A pdb=" N GLU C 255 " --> pdb=" O GLY C 252 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 256' Processing helix chain 'C' and resid 257 through 267 removed outlier: 3.993A pdb=" N ARG C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.754A pdb=" N ASP B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.661A pdb=" N GLN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B 177 " --> pdb=" O PRO B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 173 through 177' Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.609A pdb=" N GLU B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 257 through 267 removed outlier: 3.993A pdb=" N ARG B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.753A pdb=" N ASP A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.661A pdb=" N GLN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 177 " --> pdb=" O PRO A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 177' Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.610A pdb=" N GLU A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.994A pdb=" N ARG A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 8 removed outlier: 3.668A pdb=" N GLY C 63 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY C 73 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 62 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG C 71 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.357A pdb=" N ARG C 41 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU C 25 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR C 39 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 190 through 191 removed outlier: 5.676A pdb=" N ILE C 303 " --> pdb=" O ASN C 322 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN C 322 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 202 through 203 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 8 removed outlier: 3.667A pdb=" N GLY B 63 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 73 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 62 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG B 71 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 26 removed outlier: 6.357A pdb=" N ARG B 41 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 25 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR B 39 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 190 through 191 removed outlier: 5.675A pdb=" N ILE B 303 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN B 322 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 8 removed outlier: 3.667A pdb=" N GLY A 63 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 73 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 62 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG A 71 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 22 through 26 removed outlier: 6.357A pdb=" N ARG A 41 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 25 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR A 39 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 190 through 191 removed outlier: 5.675A pdb=" N ILE A 303 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN A 322 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 202 through 203 81 hydrogen bonds defined for protein. 225 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: 1.78 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2539 1.34 - 1.46: 1375 1.46 - 1.58: 3460 1.58 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 7443 Sorted by residual: bond pdb=" C LEU A 218 " pdb=" N PRO A 219 " ideal model delta sigma weight residual 1.341 1.362 -0.021 1.60e-02 3.91e+03 1.76e+00 bond pdb=" CB PRO A 86 " pdb=" CG PRO A 86 " ideal model delta sigma weight residual 1.492 1.426 0.066 5.00e-02 4.00e+02 1.76e+00 bond pdb=" CB PRO B 86 " pdb=" CG PRO B 86 " ideal model delta sigma weight residual 1.492 1.426 0.066 5.00e-02 4.00e+02 1.75e+00 bond pdb=" CB PRO C 86 " pdb=" CG PRO C 86 " ideal model delta sigma weight residual 1.492 1.426 0.066 5.00e-02 4.00e+02 1.75e+00 bond pdb=" C LEU B 218 " pdb=" N PRO B 219 " ideal model delta sigma weight residual 1.341 1.362 -0.021 1.60e-02 3.91e+03 1.66e+00 ... (remaining 7438 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.64: 234 106.64 - 113.85: 4131 113.85 - 121.07: 3250 121.07 - 128.28: 2381 128.28 - 135.49: 57 Bond angle restraints: 10053 Sorted by residual: angle pdb=" N VAL B 14 " pdb=" CA VAL B 14 " pdb=" C VAL B 14 " ideal model delta sigma weight residual 108.95 101.03 7.92 1.65e+00 3.67e-01 2.31e+01 angle pdb=" N VAL A 14 " pdb=" CA VAL A 14 " pdb=" C VAL A 14 " ideal model delta sigma weight residual 108.95 101.07 7.88 1.65e+00 3.67e-01 2.28e+01 angle pdb=" N VAL C 14 " pdb=" CA VAL C 14 " pdb=" C VAL C 14 " ideal model delta sigma weight residual 108.95 101.09 7.86 1.65e+00 3.67e-01 2.27e+01 angle pdb=" CA PRO A 85 " pdb=" C PRO A 85 " pdb=" N PRO A 86 " ideal model delta sigma weight residual 117.93 123.03 -5.10 1.20e+00 6.94e-01 1.81e+01 angle pdb=" CA PRO B 85 " pdb=" C PRO B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 117.93 123.00 -5.07 1.20e+00 6.94e-01 1.78e+01 ... (remaining 10048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 4254 14.28 - 28.55: 249 28.55 - 42.83: 9 42.83 - 57.10: 0 57.10 - 71.38: 6 Dihedral angle restraints: 4518 sinusoidal: 1830 harmonic: 2688 Sorted by residual: dihedral pdb=" CA PHE B 199 " pdb=" C PHE B 199 " pdb=" N ASP B 200 " pdb=" CA ASP B 200 " ideal model delta harmonic sigma weight residual 180.00 154.32 25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PHE A 199 " pdb=" C PHE A 199 " pdb=" N ASP A 200 " pdb=" CA ASP A 200 " ideal model delta harmonic sigma weight residual 180.00 154.36 25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA PHE C 199 " pdb=" C PHE C 199 " pdb=" N ASP C 200 " pdb=" CA ASP C 200 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 4515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 824 0.058 - 0.117: 229 0.117 - 0.175: 61 0.175 - 0.233: 8 0.233 - 0.292: 3 Chirality restraints: 1125 Sorted by residual: chirality pdb=" CB ILE C 105 " pdb=" CA ILE C 105 " pdb=" CG1 ILE C 105 " pdb=" CG2 ILE C 105 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE B 105 " pdb=" CA ILE B 105 " pdb=" CG1 ILE B 105 " pdb=" CG2 ILE B 105 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1122 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 187 " 0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 188 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 187 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO B 188 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 188 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 188 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 187 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO C 188 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 188 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 188 " 0.035 5.00e-02 4.00e+02 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1109 2.77 - 3.30: 6094 3.30 - 3.83: 11304 3.83 - 4.37: 13014 4.37 - 4.90: 22207 Nonbonded interactions: 53728 Sorted by model distance: nonbonded pdb=" OG1 THR B 79 " pdb=" OG1 THR B 92 " model vdw 2.234 2.440 nonbonded pdb=" OG1 THR C 79 " pdb=" OG1 THR C 92 " model vdw 2.234 2.440 nonbonded pdb=" OG1 THR A 79 " pdb=" OG1 THR A 92 " model vdw 2.234 2.440 nonbonded pdb=" O THR B 104 " pdb=" OG1 THR B 153 " model vdw 2.246 2.440 nonbonded pdb=" O THR C 104 " pdb=" OG1 THR C 153 " model vdw 2.247 2.440 ... (remaining 53723 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4530 2.51 5 N 1362 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.000 Extract box with map and model: 7.770 Check model and map are aligned: 0.120 Process input model: 22.310 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 7443 Z= 0.355 Angle : 1.067 10.493 10053 Z= 0.571 Chirality : 0.059 0.292 1125 Planarity : 0.006 0.063 1326 Dihedral : 8.739 71.380 2796 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.59 % Favored : 86.41 % Rotamer Outliers : 0.39 % 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: -5.23 (0.22), residues: 942 helix: -5.41 (0.09), residues: 90 sheet: -3.34 (0.32), residues: 213 loop : -3.43 (0.20), residues: 639 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 223 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 226 average time/residue: 0.2897 time to fit residues: 79.8388 Evaluate side-chains 132 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 30.0000 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 40.0000 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 50.0000 chunk 54 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN C 242 HIS B 81 GLN B 126 ASN B 242 HIS A 126 ASN A 242 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 7443 Z= 0.281 Angle : 0.737 7.089 10053 Z= 0.374 Chirality : 0.047 0.132 1125 Planarity : 0.005 0.045 1326 Dihedral : 7.034 25.827 1059 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer Outliers : 3.73 % 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: -5.17 (0.22), residues: 942 helix: -5.27 (0.15), residues: 96 sheet: -3.59 (0.26), residues: 267 loop : -3.11 (0.22), residues: 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 0.890 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 21 residues processed: 165 average time/residue: 0.2559 time to fit residues: 53.3345 Evaluate side-chains 158 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0667 time to fit residues: 3.7869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 23 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN A 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7443 Z= 0.229 Angle : 0.702 9.068 10053 Z= 0.352 Chirality : 0.046 0.135 1125 Planarity : 0.005 0.043 1326 Dihedral : 6.518 24.969 1059 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer Outliers : 1.29 % 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 (0.23), residues: 942 helix: -5.17 (0.16), residues: 96 sheet: -3.35 (0.28), residues: 279 loop : -2.98 (0.22), residues: 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 0.930 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 149 average time/residue: 0.2610 time to fit residues: 49.0680 Evaluate side-chains 136 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0726 time to fit residues: 1.7340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 56 optimal weight: 40.0000 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 HIS B 126 ASN A 179 GLN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 7443 Z= 0.426 Angle : 0.826 10.095 10053 Z= 0.420 Chirality : 0.049 0.142 1125 Planarity : 0.007 0.048 1326 Dihedral : 7.014 26.511 1059 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.92 % Favored : 84.08 % Rotamer Outliers : 3.35 % 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: -5.29 (0.22), residues: 942 helix: -5.06 (0.13), residues: 132 sheet: -3.50 (0.28), residues: 261 loop : -3.18 (0.22), residues: 549 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.897 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 20 residues processed: 147 average time/residue: 0.2697 time to fit residues: 50.0192 Evaluate side-chains 142 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0696 time to fit residues: 3.7381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 40.0000 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 7443 Z= 0.244 Angle : 0.707 8.882 10053 Z= 0.351 Chirality : 0.046 0.141 1125 Planarity : 0.005 0.040 1326 Dihedral : 6.331 24.110 1059 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.08 (0.23), residues: 942 helix: -5.01 (0.14), residues: 132 sheet: -3.24 (0.28), residues: 303 loop : -2.97 (0.23), residues: 507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 0.846 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 132 average time/residue: 0.2944 time to fit residues: 48.2060 Evaluate side-chains 117 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0688 time to fit residues: 1.3355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 7.9990 chunk 80 optimal weight: 0.0870 chunk 17 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 overall best weight: 2.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 GLN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7443 Z= 0.197 Angle : 0.663 7.563 10053 Z= 0.329 Chirality : 0.044 0.138 1125 Planarity : 0.004 0.049 1326 Dihedral : 5.967 21.850 1059 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.23), residues: 942 helix: -4.93 (0.17), residues: 132 sheet: -3.11 (0.28), residues: 303 loop : -2.89 (0.24), residues: 507 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 0.856 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 137 average time/residue: 0.2689 time to fit residues: 46.1524 Evaluate side-chains 130 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0719 time to fit residues: 2.4341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.0010 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 65 optimal weight: 0.0170 chunk 50 optimal weight: 10.0000 chunk 75 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 overall best weight: 0.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 7443 Z= 0.158 Angle : 0.653 8.550 10053 Z= 0.319 Chirality : 0.044 0.131 1125 Planarity : 0.004 0.041 1326 Dihedral : 5.573 19.944 1059 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.51 % 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: -4.72 (0.24), residues: 942 helix: -4.50 (0.26), residues: 129 sheet: -2.92 (0.28), residues: 300 loop : -2.90 (0.24), residues: 513 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.841 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 130 average time/residue: 0.2621 time to fit residues: 42.9573 Evaluate side-chains 122 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0748 time to fit residues: 1.7306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 30.0000 chunk 61 optimal weight: 0.0170 chunk 44 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 85 optimal weight: 40.0000 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS A 126 ASN A 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 7443 Z= 0.248 Angle : 0.690 8.640 10053 Z= 0.338 Chirality : 0.044 0.136 1125 Planarity : 0.005 0.043 1326 Dihedral : 5.854 21.852 1059 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer Outliers : 2.06 % 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: -4.65 (0.24), residues: 942 helix: -4.34 (0.26), residues: 129 sheet: -2.94 (0.29), residues: 291 loop : -2.84 (0.24), residues: 522 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 128 average time/residue: 0.2795 time to fit residues: 45.1223 Evaluate side-chains 125 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0718 time to fit residues: 2.6132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN A 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 7443 Z= 0.310 Angle : 0.738 8.901 10053 Z= 0.365 Chirality : 0.046 0.133 1125 Planarity : 0.006 0.065 1326 Dihedral : 6.229 23.948 1059 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.24), residues: 942 helix: -4.37 (0.25), residues: 129 sheet: -3.02 (0.30), residues: 291 loop : -2.94 (0.23), residues: 522 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 0.862 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 122 average time/residue: 0.3006 time to fit residues: 45.4254 Evaluate side-chains 117 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0787 time to fit residues: 1.8312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 7443 Z= 0.256 Angle : 0.696 7.436 10053 Z= 0.343 Chirality : 0.045 0.135 1125 Planarity : 0.005 0.041 1326 Dihedral : 6.017 22.374 1059 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer Outliers : 1.03 % 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: -4.73 (0.24), residues: 942 helix: -4.28 (0.27), residues: 129 sheet: -2.93 (0.29), residues: 303 loop : -2.97 (0.24), residues: 510 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 122 average time/residue: 0.3257 time to fit residues: 48.6148 Evaluate side-chains 122 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0684 time to fit residues: 1.9590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 HIS ** 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 = 0.4350 r_free = 0.4350 target = 0.221014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.187501 restraints weight = 7965.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.184908 restraints weight = 11460.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.182258 restraints weight = 11596.539| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7443 Z= 0.179 Angle : 0.672 9.162 10053 Z= 0.327 Chirality : 0.044 0.131 1125 Planarity : 0.005 0.061 1326 Dihedral : 5.670 19.819 1059 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.25), residues: 942 helix: -4.62 (0.24), residues: 114 sheet: -2.71 (0.29), residues: 318 loop : -2.70 (0.25), residues: 510 =============================================================================== Job complete usr+sys time: 1722.26 seconds wall clock time: 32 minutes 14.99 seconds (1934.99 seconds total)