Starting phenix.real_space_refine (version: dev) on Sat Feb 18 03:10:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss5_25404/02_2023/7ss5_25404.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss5_25404/02_2023/7ss5_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_2023/7ss5_25404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss5_25404/02_2023/7ss5_25404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss5_25404/02_2023/7ss5_25404.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss5_25404/02_2023/7ss5_25404.pdb" } resolution = 2.7 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= 0.001 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 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-4877/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: 4.71, per 1000 atoms: 0.68 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: 3.45 Conformation dependent library (CDL) restraints added in 786.9 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: 2.47 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: 2.45 Time building geometry restraints manager: 3.57 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: 3507 34.80 - 69.60: 261 69.60 - 104.40: 6 104.40 - 139.20: 0 139.20 - 174.00: 2 Dihedral angle restraints: 3776 sinusoidal: 1818 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 3773 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 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. 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: 1.760 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: 7.760 Check model and map are aligned: 0.110 Process input model: 25.340 Find NCS groups from input model: 0.370 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:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 19.796 173.997 2512 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 % 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 *********************** 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 : 0.782 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 1.6459 time to fit residues: 263.3014 Evaluate side-chains 88 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0171 ------------------------------------------------------------------------------- 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: 0.7701 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 6564 Z= 0.359 Angle : 0.646 7.341 9110 Z= 0.343 Chirality : 0.044 0.131 1002 Planarity : 0.005 0.041 1032 Dihedral : 22.436 169.776 1230 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.35), residues: 672 helix: 1.91 (0.33), residues: 288 sheet: -0.39 (0.75), residues: 50 loop : 0.22 (0.37), residues: 334 *********************** 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 : 0.779 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 95 average time/residue: 1.5546 time to fit residues: 154.4273 Evaluate side-chains 87 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 2 average time/residue: 0.7055 time to fit residues: 2.5909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 52 optimal weight: 0.0570 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 overall best weight: 2.7704 ------------------------------------------------------------------------------- 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: 0.7687 moved from start: 0.2951 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= 0.248 Angle : 0.575 7.554 9110 Z= 0.302 Chirality : 0.041 0.125 1002 Planarity : 0.004 0.040 1032 Dihedral : 22.223 168.658 1230 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 3.01 % 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: 1.46 (0.34), residues: 672 helix: 2.09 (0.32), residues: 292 sheet: -0.36 (0.73), residues: 50 loop : 0.25 (0.37), residues: 330 *********************** 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 99 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.770 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 90 average time/residue: 1.5519 time to fit residues: 146.0694 Evaluate side-chains 77 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.9927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.7756 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 6564 Z= 0.358 Angle : 0.615 8.193 9110 Z= 0.325 Chirality : 0.043 0.127 1002 Planarity : 0.004 0.045 1032 Dihedral : 22.454 167.778 1230 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 3.19 % 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: 1.49 (0.34), residues: 672 helix: 2.17 (0.32), residues: 292 sheet: -0.08 (0.71), residues: 52 loop : 0.15 (0.37), residues: 328 *********************** 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 95 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.743 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 88 average time/residue: 1.4342 time to fit residues: 132.3250 Evaluate side-chains 72 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.1955 time to fit residues: 1.1367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 27 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 0.0060 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 overall best weight: 3.5602 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 6564 Z= 0.285 Angle : 0.575 7.521 9110 Z= 0.303 Chirality : 0.042 0.126 1002 Planarity : 0.004 0.038 1032 Dihedral : 22.294 167.945 1230 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 2.48 % 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: 1.58 (0.34), residues: 672 helix: 2.29 (0.32), residues: 292 sheet: -0.17 (0.71), residues: 52 loop : 0.19 (0.37), residues: 328 *********************** 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 89 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.776 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 84 average time/residue: 1.5306 time to fit residues: 134.9628 Evaluate side-chains 75 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.7626 time to fit residues: 2.7449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 0.0570 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- 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: 0.7653 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6564 Z= 0.172 Angle : 0.550 9.363 9110 Z= 0.285 Chirality : 0.040 0.127 1002 Planarity : 0.003 0.027 1032 Dihedral : 22.207 168.172 1230 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 2.13 % 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: 1.85 (0.35), residues: 672 helix: 2.54 (0.32), residues: 292 sheet: -0.31 (0.70), residues: 52 loop : 0.36 (0.38), residues: 328 *********************** 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 87 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.752 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 85 average time/residue: 1.4459 time to fit residues: 129.2486 Evaluate side-chains 73 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.1185 time to fit residues: 1.1625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 0.0670 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- 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 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6564 Z= 0.185 Angle : 0.554 7.079 9110 Z= 0.289 Chirality : 0.040 0.127 1002 Planarity : 0.003 0.029 1032 Dihedral : 22.222 167.872 1230 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 3.01 % 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: 1.90 (0.35), residues: 672 helix: 2.60 (0.32), residues: 292 sheet: -0.27 (0.69), residues: 52 loop : 0.37 (0.38), residues: 328 *********************** 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 84 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.731 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 79 average time/residue: 1.3071 time to fit residues: 108.9856 Evaluate side-chains 73 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.1223 time to fit residues: 1.1152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6564 Z= 0.192 Angle : 0.577 9.243 9110 Z= 0.297 Chirality : 0.040 0.126 1002 Planarity : 0.003 0.026 1032 Dihedral : 22.243 168.088 1230 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 2.48 % 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: 2.63 (0.32), residues: 292 sheet: -0.24 (0.69), residues: 52 loop : 0.42 (0.38), residues: 328 *********************** 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: 14 poor density : 71 time to evaluate : 1.104 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 81 average time/residue: 1.4947 time to fit residues: 126.8159 Evaluate side-chains 77 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1664 time to fit residues: 1.4440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4078 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= 0.218 Angle : 0.579 7.316 9110 Z= 0.302 Chirality : 0.040 0.125 1002 Planarity : 0.003 0.027 1032 Dihedral : 22.369 173.226 1230 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 2.13 % 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: 1.91 (0.35), residues: 672 helix: 2.60 (0.32), residues: 292 sheet: -0.26 (0.69), residues: 52 loop : 0.38 (0.38), residues: 328 *********************** 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 80 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.780 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 76 average time/residue: 1.3998 time to fit residues: 112.1663 Evaluate side-chains 76 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.1996 time to fit residues: 1.8039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 0.043 6564 Z= 0.283 Angle : 0.608 7.497 9110 Z= 0.319 Chirality : 0.042 0.129 1002 Planarity : 0.004 0.027 1032 Dihedral : 22.474 173.140 1230 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.95 % 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: 1.79 (0.35), residues: 672 helix: 2.49 (0.32), residues: 292 sheet: -0.28 (0.69), residues: 52 loop : 0.31 (0.37), residues: 328 ********************** 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 76 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.802 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 73 average time/residue: 1.3003 time to fit residues: 100.2261 Evaluate side-chains 71 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.9565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.117370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.092122 restraints weight = 12105.709| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.59 r_work: 0.3029 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6564 Z= 0.207 Angle : 0.584 7.468 9110 Z= 0.303 Chirality : 0.040 0.129 1002 Planarity : 0.003 0.028 1032 Dihedral : 22.381 172.856 1230 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.35), residues: 672 helix: 2.52 (0.32), residues: 292 sheet: -0.28 (0.69), residues: 52 loop : 0.33 (0.38), residues: 328 =============================================================================== Job complete usr+sys time: 2668.29 seconds wall clock time: 48 minutes 3.88 seconds (2883.88 seconds total)