Starting phenix.real_space_refine on Tue Feb 13 16:39:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss5_25404/02_2024/7ss5_25404.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss5_25404/02_2024/7ss5_25404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss5_25404/02_2024/7ss5_25404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss5_25404/02_2024/7ss5_25404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss5_25404/02_2024/7ss5_25404.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss5_25404/02_2024/7ss5_25404.pdb" } resolution = 2.7 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 Ca 6 9.91 5 P 48 5.49 5 S 18 5.16 5 C 3844 2.51 5 N 1140 2.21 5 O 1871 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 321": "OD1" <-> "OD2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 321": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6927 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 492 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "B" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 492 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 254 Classifications: {'water': 254} Link IDs: {None: 253} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "B" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Time building chain proxies: 4.53, per 1000 atoms: 0.65 Number of scatterers: 6927 At special positions: 0 Unit cell: (83, 86.32, 106.24, 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) Ca 6 19.99 S 18 16.00 P 48 15.00 O 1871 8.00 N 1140 7.00 C 3844 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: 3.32 Conformation dependent library (CDL) restraints added in 961.4 milliseconds 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 51.8% alpha, 8.3% beta 18 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.653A pdb=" N ARG A 18 " --> pdb=" O THR A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 90 through 123 Processing helix chain 'A' and resid 161 through 178 removed outlier: 4.050A pdb=" N VAL A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.983A pdb=" N TRP A 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 221 through 226 removed outlier: 4.029A pdb=" N ARG A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 226' Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 250 through 265 removed outlier: 4.015A pdb=" N LEU A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 318 through 334 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.653A pdb=" N ARG B 18 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 90 through 123 Processing helix chain 'B' and resid 161 through 178 removed outlier: 4.049A pdb=" N VAL B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.983A pdb=" N TRP B 204 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.028A pdb=" N ARG B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 250 through 265 removed outlier: 4.015A pdb=" N LEU B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' 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 145 through 149 removed outlier: 6.822A pdb=" N VAL A 193 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 235 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLU A 276 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA A 238 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS A 278 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA A 240 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N LEU A 280 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 9.867A pdb=" N LYS A 242 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N TYR A 314 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 277 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22 Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 149 removed outlier: 6.822A pdb=" N VAL B 193 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE B 235 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N GLU B 276 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 238 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS B 278 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 240 " --> pdb=" O HIS B 278 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N LEU B 280 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N LYS B 242 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N TYR B 314 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) 226 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1665 1.33 - 1.45: 1397 1.45 - 1.57: 3376 1.57 - 1.69: 94 1.69 - 1.81: 32 Bond restraints: 6564 Sorted by residual: bond pdb=" CA LEU A 296 " pdb=" C LEU A 296 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.10e-02 8.26e+03 2.44e+00 bond pdb=" CD ARG A 303 " pdb=" NE ARG A 303 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.40e+00 bond pdb=" CA LEU B 296 " pdb=" C LEU B 296 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.10e-02 8.26e+03 2.39e+00 bond pdb=" CD ARG B 303 " pdb=" NE ARG B 303 " ideal model delta sigma weight residual 1.458 1.479 -0.021 1.40e-02 5.10e+03 2.33e+00 bond pdb=" CA TYR B 297 " pdb=" C TYR B 297 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.10e-02 8.26e+03 2.08e+00 ... (remaining 6559 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.02: 496 107.02 - 113.78: 3508 113.78 - 120.54: 2671 120.54 - 127.30: 2303 127.30 - 134.06: 132 Bond angle restraints: 9110 Sorted by residual: angle pdb=" N GLU A 292 " pdb=" CA GLU A 292 " pdb=" C GLU A 292 " ideal model delta sigma weight residual 110.68 102.90 7.78 1.39e+00 5.18e-01 3.13e+01 angle pdb=" N GLU B 292 " pdb=" CA GLU B 292 " pdb=" C GLU B 292 " ideal model delta sigma weight residual 110.68 102.94 7.74 1.39e+00 5.18e-01 3.10e+01 angle pdb=" N ARG A 311 " pdb=" CA ARG A 311 " pdb=" C ARG A 311 " ideal model delta sigma weight residual 111.28 117.33 -6.05 1.09e+00 8.42e-01 3.08e+01 angle pdb=" N ARG B 311 " pdb=" CA ARG B 311 " pdb=" C ARG B 311 " ideal model delta sigma weight residual 111.28 117.31 -6.03 1.09e+00 8.42e-01 3.06e+01 angle pdb=" N GLY B 58 " pdb=" CA GLY B 58 " pdb=" C GLY B 58 " ideal model delta sigma weight residual 112.73 107.77 4.96 1.20e+00 6.94e-01 1.71e+01 ... (remaining 9105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 3547 34.80 - 69.60: 261 69.60 - 104.40: 6 104.40 - 139.20: 0 139.20 - 174.00: 2 Dihedral angle restraints: 3816 sinusoidal: 1858 harmonic: 1958 Sorted by residual: dihedral pdb=" C ALA B 55 " pdb=" N ALA B 55 " pdb=" CA ALA B 55 " pdb=" CB ALA B 55 " ideal model delta harmonic sigma weight residual -122.60 -111.34 -11.26 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C ALA A 55 " pdb=" N ALA A 55 " pdb=" CA ALA A 55 " pdb=" CB ALA A 55 " ideal model delta harmonic sigma weight residual -122.60 -111.36 -11.24 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" CA GLN B 129 " pdb=" C GLN B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 913 0.077 - 0.155: 83 0.155 - 0.232: 4 0.232 - 0.309: 0 0.309 - 0.386: 2 Chirality restraints: 1002 Sorted by residual: chirality pdb=" CA ALA B 55 " pdb=" N ALA B 55 " pdb=" C ALA B 55 " pdb=" CB ALA B 55 " both_signs ideal model delta sigma weight residual False 2.48 2.87 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA ALA A 55 " pdb=" N ALA A 55 " pdb=" C ALA A 55 " pdb=" CB ALA A 55 " both_signs ideal model delta sigma weight residual False 2.48 2.87 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA GLU B 292 " pdb=" N GLU B 292 " pdb=" C GLU B 292 " pdb=" CB GLU B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.12e-01 ... (remaining 999 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 55 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C ALA B 55 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA B 55 " 0.015 2.00e-02 2.50e+03 pdb=" N SER B 56 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 55 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C ALA A 55 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA A 55 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 56 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 155 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ASP A 155 " 0.025 2.00e-02 2.50e+03 pdb=" O ASP A 155 " -0.009 2.00e-02 2.50e+03 pdb=" N TRP A 156 " -0.008 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 441 2.72 - 3.27: 6424 3.27 - 3.81: 12394 3.81 - 4.36: 16446 4.36 - 4.90: 24478 Nonbonded interactions: 60183 Sorted by model distance: nonbonded pdb=" CG GLU A 301 " pdb=" CG GLU B 301 " model vdw 2.179 3.840 nonbonded pdb=" CA GLY B 266 " pdb=" OH TYR B 297 " model vdw 2.241 3.440 nonbonded pdb=" CA GLY A 266 " pdb=" OH TYR A 297 " model vdw 2.242 3.440 nonbonded pdb=" O HOH B 553 " pdb=" O HOH B 666 " model vdw 2.269 2.440 nonbonded pdb=" OD1 ASN B 92 " pdb=" O HOH B 501 " model vdw 2.287 2.440 ... (remaining 60178 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' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.780 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.030 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 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 0.035 6564 Z= 0.191 Angle : 0.633 7.778 9110 Z= 0.381 Chirality : 0.046 0.386 1002 Planarity : 0.004 0.033 1032 Dihedral : 19.806 173.997 2552 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.32 % 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: 0.76 (0.34), residues: 672 helix: 1.32 (0.34), residues: 280 sheet: -0.62 (0.74), residues: 50 loop : 0.09 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 156 HIS 0.002 0.001 HIS A 81 PHE 0.021 0.001 PHE A 171 TYR 0.014 0.001 TYR A 64 ARG 0.001 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.717 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 1.6387 time to fit residues: 262.3199 Evaluate side-chains 88 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 129 GLN A 307 HIS B 112 ASN B 227 GLN B 307 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6564 Z= 0.359 Angle : 0.654 7.431 9110 Z= 0.347 Chirality : 0.044 0.136 1002 Planarity : 0.005 0.042 1032 Dihedral : 22.422 171.834 1270 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.66 % Allowed : 13.30 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.34), residues: 672 helix: 1.89 (0.32), residues: 288 sheet: -0.39 (0.74), residues: 50 loop : 0.24 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 156 HIS 0.003 0.001 HIS A 81 PHE 0.013 0.001 PHE A 54 TYR 0.015 0.002 TYR A 5 ARG 0.006 0.001 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.692 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 94 average time/residue: 1.4672 time to fit residues: 144.2916 Evaluate side-chains 77 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 220 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 0.0040 chunk 52 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN B 30 ASN B 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6564 Z= 0.311 Angle : 0.600 9.491 9110 Z= 0.315 Chirality : 0.042 0.126 1002 Planarity : 0.004 0.037 1032 Dihedral : 22.252 169.460 1270 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.48 % Allowed : 15.96 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.34), residues: 672 helix: 2.05 (0.32), residues: 292 sheet: -0.42 (0.72), residues: 50 loop : 0.21 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 156 HIS 0.002 0.001 HIS B 81 PHE 0.008 0.001 PHE B 54 TYR 0.013 0.002 TYR A 5 ARG 0.010 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.757 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 85 average time/residue: 1.5630 time to fit residues: 138.7213 Evaluate side-chains 79 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 321 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6564 Z= 0.316 Angle : 0.599 8.436 9110 Z= 0.314 Chirality : 0.042 0.126 1002 Planarity : 0.004 0.045 1032 Dihedral : 22.293 169.133 1270 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.19 % Allowed : 16.31 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.34), residues: 672 helix: 2.16 (0.32), residues: 292 sheet: -0.16 (0.70), residues: 52 loop : 0.17 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 156 HIS 0.002 0.001 HIS A 307 PHE 0.009 0.001 PHE B 54 TYR 0.013 0.002 TYR A 5 ARG 0.008 0.001 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.734 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 94 average time/residue: 1.4863 time to fit residues: 145.9816 Evaluate side-chains 78 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 220 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 46 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 224 GLN B 40 GLN B 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6564 Z= 0.340 Angle : 0.600 6.603 9110 Z= 0.319 Chirality : 0.043 0.126 1002 Planarity : 0.004 0.041 1032 Dihedral : 22.366 169.011 1270 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.01 % Allowed : 16.49 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.34), residues: 672 helix: 2.22 (0.32), residues: 292 sheet: -0.14 (0.70), residues: 52 loop : 0.18 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 PHE 0.009 0.001 PHE B 54 TYR 0.015 0.002 TYR A 223 ARG 0.009 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.739 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 87 average time/residue: 1.5209 time to fit residues: 138.4774 Evaluate side-chains 75 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6564 Z= 0.222 Angle : 0.565 6.403 9110 Z= 0.298 Chirality : 0.041 0.126 1002 Planarity : 0.004 0.026 1032 Dihedral : 22.266 169.510 1270 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.66 % Allowed : 18.09 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.35), residues: 672 helix: 2.39 (0.32), residues: 292 sheet: -0.11 (0.73), residues: 48 loop : 0.31 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 PHE 0.008 0.001 PHE B 54 TYR 0.011 0.001 TYR B 297 ARG 0.006 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.784 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 84 average time/residue: 1.3981 time to fit residues: 123.3143 Evaluate side-chains 74 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 0.0770 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6564 Z= 0.165 Angle : 0.555 8.864 9110 Z= 0.288 Chirality : 0.039 0.127 1002 Planarity : 0.003 0.036 1032 Dihedral : 22.144 171.145 1270 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.60 % Allowed : 19.68 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.35), residues: 672 helix: 2.62 (0.32), residues: 292 sheet: -0.22 (0.71), residues: 48 loop : 0.37 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 156 HIS 0.001 0.000 HIS A 81 PHE 0.006 0.001 PHE B 54 TYR 0.011 0.001 TYR B 297 ARG 0.009 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.682 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 86 average time/residue: 1.3415 time to fit residues: 121.2282 Evaluate side-chains 72 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 178 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 61 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 62 optimal weight: 0.4980 chunk 37 optimal weight: 10.0000 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6564 Z= 0.188 Angle : 0.563 6.729 9110 Z= 0.294 Chirality : 0.040 0.126 1002 Planarity : 0.003 0.029 1032 Dihedral : 22.271 174.617 1270 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.84 % Allowed : 18.62 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.35), residues: 672 helix: 2.65 (0.32), residues: 292 sheet: -0.28 (0.69), residues: 48 loop : 0.38 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 156 HIS 0.001 0.001 HIS A 81 PHE 0.006 0.001 PHE B 54 TYR 0.012 0.001 TYR A 223 ARG 0.007 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.777 Fit side-chains REVERT: A 64 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7714 (t80) outliers start: 16 outliers final: 10 residues processed: 79 average time/residue: 1.2179 time to fit residues: 101.7268 Evaluate side-chains 80 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 321 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6564 Z= 0.238 Angle : 0.605 9.022 9110 Z= 0.311 Chirality : 0.041 0.126 1002 Planarity : 0.003 0.026 1032 Dihedral : 22.330 173.680 1270 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.95 % Allowed : 20.04 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.35), residues: 672 helix: 2.61 (0.32), residues: 292 sheet: -0.46 (0.67), residues: 52 loop : 0.30 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 PHE 0.007 0.001 PHE B 54 TYR 0.017 0.002 TYR B 5 ARG 0.007 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.714 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 78 average time/residue: 1.3401 time to fit residues: 109.9063 Evaluate side-chains 76 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 55 optimal weight: 0.0970 chunk 5 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6564 Z= 0.165 Angle : 0.569 8.268 9110 Z= 0.294 Chirality : 0.039 0.134 1002 Planarity : 0.003 0.029 1032 Dihedral : 22.273 176.956 1270 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.60 % Allowed : 20.21 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.35), residues: 672 helix: 2.71 (0.32), residues: 292 sheet: -0.29 (0.70), residues: 48 loop : 0.41 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 156 HIS 0.001 0.000 HIS A 278 PHE 0.007 0.001 PHE B 54 TYR 0.011 0.001 TYR B 297 ARG 0.007 0.000 ARG B 311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.728 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 1.2125 time to fit residues: 120.2726 Evaluate side-chains 87 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 0.0270 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.096474 restraints weight = 12083.656| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.62 r_work: 0.3127 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6564 Z= 0.179 Angle : 0.604 8.147 9110 Z= 0.315 Chirality : 0.040 0.151 1002 Planarity : 0.003 0.029 1032 Dihedral : 22.317 176.792 1270 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.71 % Allowed : 21.99 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.35), residues: 672 helix: 2.41 (0.32), residues: 304 sheet: -0.17 (0.70), residues: 48 loop : 0.30 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 156 HIS 0.001 0.000 HIS A 278 PHE 0.021 0.001 PHE B 171 TYR 0.016 0.001 TYR A 5 ARG 0.007 0.000 ARG B 311 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2845.20 seconds wall clock time: 51 minutes 11.79 seconds (3071.79 seconds total)